Last updated: 2021-08-26

Checks: 7 0

Knit directory: IITA_2021GS/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20210504)

The command set.seed(20210504) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: c2c7dae

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version c2c7dae. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    data/.DS_Store

Untracked files:
    Untracked:  data/DatabaseDownload_2021Aug08/
    Untracked:  data/DatabaseDownload_2021May04/
    Untracked:  data/GBSdataMasterList_31818.csv
    Untracked:  data/IITA_GBStoPhenoMaster_33018.csv
    Untracked:  data/NRCRI_GBStoPhenoMaster_40318.csv
    Untracked:  data/PedigreeGeneticGainCycleTime_aafolabi_01122020.xls
    Untracked:  data/Report-DCas21-6038/
    Untracked:  data/blups_forGP.rds
    Untracked:  data/chr1_RefPanelAndGSprogeny_ReadyForGP_72719.fam
    Untracked:  data/dosages_IITA_2021Aug09.rds
    Untracked:  data/haps_IITA_2021Aug09.rds
    Untracked:  data/recombFreqMat_1minus2c_2021Aug02.qs
    Untracked:  output/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/03-validatePedigree.Rmd) and HTML (docs/03-validatePedigree.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	19c3a38	wolfemd	2021-08-19	Build site.
html	1c03315	wolfemd	2021-08-11	Build site.
Rmd	e4df79f	wolfemd	2021-08-11	Completed IITA_2021GS pipeline including imputation and genomic prediction. Last bit of cross-validation and cross-prediction finishes in 24 hrs.
html	934141c	wolfemd	2021-07-14	Build site.
html	e66bdad	wolfemd	2021-06-10	Build site.
Rmd	a8452ba	wolfemd	2021-06-10	Initial build of the entire page upon completion of all

Previous step

Get BLUPs combining all trial data: Combine data from all trait-trials to get BLUPs for downstream genomic prediction. Fit mixed-model to multi-trial dataset and extract BLUPs, de-regressed BLUPs and weights. Include two rounds of outlier removal.

Read pedigree

Read the pedigree I downloaded for IITA

library(tidyverse); library(magrittr)

ped<-read_delim(here::here("data/DatabaseDownload_2021May04","pedigree.txt"),
                delim = "\t")
ped_tms20<-readxl::read_xlsx(here::here("data/DatabaseDownload_2021Aug08","Pedigree.xlsx"))
ped %<>% 
  select(-Cross_Type) %>% 
  bind_rows(ped_tms20 %>% 
              select(Accession_name,Pedigree) %>% 
              rename(Accession=Accession_name) %>% 
              separate(Pedigree,c("Female_Parent","Male_Parent"),"/"))
#rm(ped_tms20)

Filter: Keep only complete pedigree records.

ped %<>% 
  filter(!is.na(Female_Parent),
         !is.na(Male_Parent),
         Female_Parent!="?",
         Male_Parent!="?") %>% 
  distinct

Number of full-sib families?

ped %>% distinct(Female_Parent,Male_Parent) %>% nrow()

[1] 1826

Summarize distribution of full-sib family sizes

ped %>%   
  count(Female_Parent,Male_Parent) %>% arrange(desc(n))  %>%  summary(.$n)

 Female_Parent      Male_Parent              n          
 Length:1826        Length:1826        Min.   :  1.000  
 Class :character   Class :character   1st Qu.:  1.000  
 Mode  :character   Mode  :character   Median :  2.000  
                                       Mean   :  5.059  
                                       3rd Qu.:  6.000  
                                       Max.   :276.000

ped %>% head

# A tibble: 6 × 3
  Accession       Female_Parent      Male_Parent       
  <chr>           <chr>              <chr>             
1 TMS13F1002P0001 IITA-TMS-IBA930265 IITA-TMS-MOK980068
2 TMS13F1002P0002 IITA-TMS-IBA930265 IITA-TMS-MOK980068
3 TMS13F1002P0003 IITA-TMS-IBA930265 IITA-TMS-MOK980068
4 TMS13F1002P0004 IITA-TMS-IBA930265 IITA-TMS-MOK980068
5 TMS13F1002P0005 IITA-TMS-IBA930265 IITA-TMS-MOK980068
6 TMS13F1002P0006 IITA-TMS-IBA930265 IITA-TMS-MOK980068

Match SNP-to-pedigree names

Goal is to identify DNA samples names for listed accessions and parents in the pedigree. Important to choose same samples used in genomic predictions where possible, esp. phenotyped training clones.

However, there may be non-phenotyped clones that are genotyped genomic selection progeny, which I still want in my analysis.

First with the union of the parent and accession IDs in the pedigree.

pednames<-union(ped$Accession,union(ped$Female_Parent,ped$Male_Parent)) %>% 
  tibble(germplasmName=.)
pednames$germplasmName %>% length # number of names in ped

[1] 9568

Add a “Cohort” variable corresponding to the genetic groups or cycles in the germplasm.

pednames %<>%
  mutate(Cohort=NA,
         Cohort=ifelse(grepl("TMS20",germplasmName,ignore.case = T),"TMS20",
                       ifelse(grepl("TMS19",germplasmName,ignore.case = T),"TMS19",
                              ifelse(grepl("TMS18",germplasmName,ignore.case = T),"TMS18",
                                     ifelse(grepl("TMS17",germplasmName,ignore.case = T),"TMS17",
                                            ifelse(grepl("TMS16",germplasmName,ignore.case = T),"TMS16",
                                                   ifelse(grepl("TMS15",germplasmName,ignore.case = T),"TMS15",
                                                          ifelse(grepl("TMS14",germplasmName,ignore.case = T),"TMS14",
                                                                 ifelse(grepl("TMS13|2013_",germplasmName,ignore.case = T),"TMS13","GGetc")))))))))
pednames %>% 
  count(Cohort)

# A tibble: 9 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    400
2 TMS13   2629
3 TMS14   1981
4 TMS15   1240
5 TMS16      6
6 TMS17     70
7 TMS18   2394
8 TMS19    178
9 TMS20    670

The names in the pedigree downloaded from cassavabase should match the names in the germplasmName variable in the plot-basis pheno data, also downloaded from cassavabase. From that plot-basis data, make a data.frame of the unique germplasmName-to-FullSampleName matches, where FullSampleName is the column with names matching VCF files / DNA samples.

dbdata<-readRDS(here::here("output","IITA_ExptDesignsDetected_2021Aug08.rds"))
phenos2genos<-dbdata %>% 
  distinct(GID,germplasmName,FullSampleName) %>% 
  filter(!is.na(FullSampleName))
phenos2genos %>% head

# A tibble: 6 × 3
  germplasmName     FullSampleName           GID                     
  <chr>             <chr>                    <chr>                   
1 IITA-TMS-IBA30572 I30572:250253643         I30572:250253643        
2 IITA-TMS-IBA30572 IITA-TMS-IBA30572_A35468 IITA-TMS-IBA30572_A35468
3 IITA-TMS-IBA30572 IITA-TMS-IBA30572_A35591 IITA-TMS-IBA30572_A35591
4 IITA-TMS-IBA30572 IITA-TMS-IBA30572_A35546 IITA-TMS-IBA30572_A35546
5 IITA-TMS-IBA30572 IITA-TMS-IBA30572_A35594 IITA-TMS-IBA30572_A35594
6 IITA-TMS-IBA30572 IITA-TMS-IBA30572_A35750 IITA-TMS-IBA30572_A35750

How many from each cohort in the pednames match a germplasmName with a FullSampleName in the plot-basis trial data?

pednames %>%
  inner_join(phenos2genos) %>% 
  count(Cohort)

# A tibble: 9 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    302
2 TMS13   2467
3 TMS14   1536
4 TMS15    867
5 TMS16      1
6 TMS17     36
7 TMS18   1400
8 TMS19    178
9 TMS20    674

I want haplotypes of genotyped progeny in the pedigree even if they aren’t phenotyped.

The *.fam file for the RefPanelAndGSprogeny VCF I will ultimately use to extract haplotypes and do predictions with is already in the data/ directory because it’s used in the standard match-genos-to-phenos step.

gids_in_fam<-read.table(here::here("data",
                                   "chr1_RefPanelAndGSprogeny_ReadyForGP_72719.fam"), 
                        stringsAsFactors = F, header = F)$V2
length(gids_in_fam)

[1] 21856

Split the names based on a “:” for the GBS samples, and “_A” seems to work (for IITA) to split the DArT sample ID from the germplasmName for DArTseqLD samples. The suffix / ID added to DNA sample names at DARt seems to vary depending on what gets submitted to them. GBS-era samples (almost) 100% had the “:” separator.

gids_in_fam %<>%
  tibble(FullSampleName=.) %>%
  separate(FullSampleName,c("germplasmName","DNA_ID"),":|_A",remove = F) %>% 
  select(-DNA_ID)
gids_in_fam %>%
  filter(grepl("TMS18",FullSampleName)) %>% nrow()

[1] 2420

There are also TMS20 in the latest DArT report and the DB sourced ped contains matches to the DARt sample names.

gids_in_fam<-gids_in_fam %>% 
  bind_rows(ped_tms20 %>% 
              select(Accession_name,Lab_ID) %>% 
              rename(germplasmName=Accession_name,
                     FullSampleName=Lab_ID) %>% 
              mutate(FullSampleName=gsub("\\.","_",FullSampleName)))
gids_in_fam %>% head

# A tibble: 6 × 2
  FullSampleName            germplasmName  
  <chr>                     <chr>          
1 TMS15F1142P0004:250465388 TMS15F1142P0004
2 TMS15F1021P0003:250464911 TMS15F1021P0003
3 TMS15F1276P0003:250465968 TMS15F1276P0003
4 TMS15F1282P0001:250466007 TMS15F1282P0001
5 TMS15F1035P0002:250465011 TMS15F1035P0002
6 TMS15F1179P0024:250465452 TMS15F1179P0024

gids_in_fam %>%
  filter(grepl("TMS16|TMS17|TMS18|TMS19|TMS20",FullSampleName)) %>% nrow()

[1] 3713

There are 3713 “TMS16” though “TMS20” clones genotyped.

pednames2genos<-pednames %>% 
  inner_join(phenos2genos) %>% 
  bind_rows(pednames %>%
              anti_join(phenos2genos) %>% 
              inner_join(gids_in_fam))
pednames2genos %>% count(Cohort)

# A tibble: 9 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    304
2 TMS13   2469
3 TMS14   1538
4 TMS15    901
5 TMS16      1
6 TMS17     36
7 TMS18   1400
8 TMS19    178
9 TMS20    674

Are there germplasmName in the pednames2genos match table with multiple DNA samples?

pednames2genos %>% count(germplasmName) %>% arrange(desc(n))

# A tibble: 7,185 × 2
   germplasmName          n
   <chr>              <int>
 1 IITA-TMS-IBA000070    17
 2 TMEB419               16
 3 TMS13F1160P0004       16
 4 IITA-TMS-IBA30572     15
 5 IITA-TMS-IBA980581    14
 6 TMS13F1053P0010       10
 7 IITA-TMS-IBA982101     9
 8 TMS13F1343P0022        8
 9 IITA-TMS-IBA070593     7
10 TMEB693                6
# … with 7,175 more rows

Of course there are. Will need to pick.

Which pednames have BLUPs?

blups<-readRDS(file=here::here("output","IITA_blupsForModelTraining_twostage_asreml_2021Aug09.rds"))
blups %>% 
  select(Trait,blups) %>% 
  unnest(blups) %>% 
  distinct(GID) %$% GID -> gidWithBLUPs
pednames %>%
  inner_join(phenos2genos) %>% 
  filter(FullSampleName %in% gidWithBLUPs) %>% 
  count(Cohort)

# A tibble: 7 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    302
2 TMS13   2447
3 TMS14   1536
4 TMS15    845
5 TMS17     36
6 TMS18   1399
7 TMS19    178

# if there are any blups for a germplasmName
# keep only the FullSampleName/GID associated
# else keep all
pednames2genos %<>% 
  mutate(HasBLUPs=ifelse(GID %in% gidWithBLUPs,T,F)) %>% 
  nest(DNAsamples=-c(germplasmName,Cohort)) %>% 
  mutate(AnyBLUPs=map_lgl(DNAsamples,~any(.$HasBLUPs)),
         DNAsamples=ifelse(AnyBLUPs==T,
                           map(DNAsamples,~filter(.,HasBLUPs==TRUE)),
                           DNAsamples)) %>% 
  select(-AnyBLUPs) %>% 
  unnest(DNAsamples)
# Among all remaining
# Select only one GID to use for each germplasmName
pednames2genos %<>% 
  group_by(germplasmName) %>% 
  slice(1) %>% 
  ungroup()
pednames2genos %>% 
  count(Cohort)

# A tibble: 9 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    200
2 TMS13   2425
3 TMS14   1519
4 TMS15    894
5 TMS16      1
6 TMS17     36
7 TMS18   1262
8 TMS19    178
9 TMS20    670

Now make a pedigree with both Accession and parent names matching the genos (FullSampleName) rather than phenos (germplasmName).

ped2genos<-ped %>% 
  rename(germplasmName=Accession) %>% 
  inner_join(pednames2genos %>% 
               select(-GID,-HasBLUPs)) %>% 
  left_join(pednames2genos %>% 
              select(-GID,-Cohort,-HasBLUPs) %>% 
              rename(Female_Parent=germplasmName,
                     DamID=FullSampleName)) %>% 
  left_join(pednames2genos %>% 
              select(-GID,-Cohort,-HasBLUPs) %>% 
              rename(Male_Parent=germplasmName,
                     SireID=FullSampleName)) 
ped2genos %<>% 
  filter(!is.na(FullSampleName),
         !is.na(DamID),
         !is.na(SireID))
ped2genos %>% distinct# %>% filter(grepl("TMS20",germplasmName))

# A tibble: 6,257 × 7
   germplasmName  Female_Parent  Male_Parent  Cohort FullSampleName DamID SireID
   <chr>          <chr>          <chr>        <chr>  <chr>          <chr> <chr> 
 1 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_1:2… I930… M9800…
 2 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_2:2… I930… M9800…
 3 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_3:2… I930… M9800…
 4 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_4:2… I930… M9800…
 5 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_5:2… I930… M9800…
 6 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_6:2… I930… M9800…
 7 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_7:2… I930… M9800…
 8 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_8:2… I930… M9800…
 9 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_9:2… I930… M9800…
10 TMS13F1002P00… IITA-TMS-IBA9… IITA-TMS-MO… TMS13  2013_0002_10:… I930… M9800…
# … with 6,247 more rows

In the end, considering only pedigree entries where the entire trio (offspring + both parents) are genotyped, the pedigree has 6257 entries to check.

ped2genos %>% count(Cohort,DamID,SireID) %>% 
  ggplot(.,aes(x=Cohort,y=n,fill=Cohort)) + 
  geom_boxplot(notch = T) + theme_bw() +
  ggtitle("Distribution of family sizes (genotyped only)")

Version	Author	Date
1c03315	wolfemd	2021-08-11

ped2genos %>% 
  count(Cohort,DamID,SireID) %$% summary(n)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   3.000   5.298   7.000  78.000

Number of families with at least 10 genotyped members, by cohort:

ped2genos %>% 
  count(Cohort,DamID,SireID) %>% 
  filter(n>=10) %>% 
  count(Cohort)

# A tibble: 5 × 2
  Cohort     n
  <chr>  <int>
1 TMS13     95
2 TMS14     55
3 TMS15     11
4 TMS18     27
5 TMS20      8

ped2genos %>% 
  select(FullSampleName,DamID,SireID) %>% 
  write.table(.,file=here::here("output","ped2genos.txt"),row.names=F, col.names=F, quote=F)

Run plink IBD (–genome)

Alternative to the below: Could compute everything manually based on mendelian rules. Kinship coefficients directly from the relationship matrix used for prediction would also be useful, for example, the estimated inbreeding coefficient of an individual is 1/2 the relationship of its parents.

PLINK1.9 pipeline to use:

Subset whole-pop. plink file (AllChrom_RefPanelAndGSprogeny_ReadyForGP_2021Aug08) to only lines in the pedigree.
LD-prune --indep-pairwise 100 25 0.25 stringent, but somewhat arbitrary
Compute IBD-relationships --genome
Parent-offspring relationships determination (see below)

Determine parent-offspring relationship status based on plink IBD:

should have a kinship \(\hat{\pi} \approx 0.5\).
Three standard IBD probabilities are defined for each pair; the probability of sharing zero (Z0), one (Z1) or two (Z2) alleles at a randomly chosen locus IBD.
The expectation for siblings in terms of these probabilities is Z0=0.25, Z1=0.5 and Z2=0.25.
The expectation for parent-offspring pairs is Z0=0, Z1=1 and Z2=0.
Based on work I did in 2016 (never published), declare a parent-offspring pair where: Z0<0.313 and Z1>0.668.

ped2check<-read.table(file=here::here("output","ped2genos.txt"),
                      header = F, stringsAsFactors = F)

pednames<-union(ped2check$V1,union(ped2check$V2,ped2check$V3)) %>% 
  tibble(FID=0,IID=.)
write.table(pednames,file=here::here("output","pednames2keep.txt"), 
            row.names = F, col.names = F, quote = F)

Checked plink’s order-of-operations and combining –keep and –indep-pairwise in the same filter call should result in the correct ordering: first subset samples, then LD prune.

cd ~/IITA_2021GS/
export PATH=/programs/plink-1.9-x86_64-beta3.30:$PATH;
plink --bfile output/AllChrom_RefPanelAndGSprogeny_ReadyForGP_2021Aug08 \
  --keep output/pednames2keep.txt \
  --indep-pairwise 100 25 0.25 \
  --genome \
  --out output/pednames_Prune100_25_pt25;

Creates a 2GB *.genome, >6000 samples samples worth of pairwise relationships.

#cd /home/jj332_cas/marnin/implementGMSinCassava/
#export PATH=/programs/plink-1.9-x86_64-beta3.30:$PATH;
#plink --bfile output/AllChrom_RefPanelAndGSprogeny_ReadyForGP_2021Aug08 \
#  --indep-pairwise 100 25 0.25 --out output/Prune100_25_pt25;
#plink --bfile output/AllChrom_RefPanelAndGSprogeny_ReadyForGP_2021Aug08 \
#  --extract output/Prune100_25_pt25.prune.in --genome \
#  --out output/AllChrom_RefPanelAndGSprogeny_ReadyForGP_2021Aug08_Prune100_25_pt25

# That wastefully creates a >40GB `*.genome` file with all pairwise relationships.

# Brute force solution is to read that, grab the needed relationships, and delete it....

library(tidyverse); library(magrittr); library(data.table)

genome<-fread(here::here("output/", 
                         "pednames_Prune100_25_pt25.genome"),
              stringsAsFactors = F,header = T) %>% 
  as_tibble

ped2check<-read.table(file=here::here("output","ped2genos.txt"),
                      header = F, stringsAsFactors = F)

head(genome)
# A tibble: 6 × 14
#    FID1 IID1      FID2 IID2    RT       EZ    Z0    Z1     Z2 PI_HAT   PHE   DST
#   <int> <chr>    <int> <chr>   <chr> <int> <dbl> <dbl>  <dbl>  <dbl> <int> <dbl>
# 1     0 TMS15F1…     0 TMS15F… OT        0 1     0     0      0         -1 0.720
# 2     0 TMS15F1…     0 TMS15F… OT        0 0.854 0.103 0.0434 0.0948    -1 0.763
# 3     0 TMS15F1…     0 TMS15F… OT        0 0.868 0.132 0      0.0661    -1 0.718
# 4     0 TMS15F1…     0 TMS15F… OT        0 1     0     0      0         -1 0.726
# 5     0 TMS15F1…     0 TMS15F… OT        0 0.407 0.593 0      0.296     -1 0.775
# 6     0 TMS15F1…     0 TMS15F… OT        0 1     0     0      0         -1 0.715
dim(genome)
# [1] 20470401       14

ped2check_genome<-genome %>% 
  semi_join(ped2check %>% rename(IID1=V1,IID2=V2)) %>% 
  bind_rows(genome %>% semi_join(ped2check %>% rename(IID1=V2,IID2=V1))) %>% 
  bind_rows(genome %>% semi_join(ped2check %>% rename(IID1=V1,IID2=V3))) %>% 
  bind_rows(genome %>% semi_join(ped2check %>% rename(IID1=V3,IID2=V1)))
saveRDS(ped2check_genome,file=here::here("output","ped2check_genome.rds"))

cd ~/IITA_2021GS/output/;
rm pednames_Prune100_25_pt25.genome

Verify and Correct Pedigree

library(tidyverse); library(magrittr);
ped2check_genome<-readRDS(file=here::here("output","ped2check_genome.rds"))
ped2check_genome %<>% 
  select(IID1,IID2,Z0,Z1,Z2,PI_HAT)

ped2check<-read.table(file=here::here("output","ped2genos.txt"),
                      header = F, stringsAsFactors = F) %>% 
  rename(FullSampleName=V1,DamID=V2,SireID=V3)

ped2check %<>% 
  select(FullSampleName,DamID,SireID) %>% 
  inner_join(ped2check_genome %>% 
               rename(FullSampleName=IID1,DamID=IID2) %>% 
               bind_rows(ped2check_genome %>% 
                           rename(FullSampleName=IID2,DamID=IID1))) %>% 
  distinct %>% 
  mutate(ConfirmFemaleParent=case_when(Z0<0.32 & Z1>0.67~"Confirm",
                                       SireID==DamID & PI_HAT>0.6 & Z0<0.3 & Z2>0.32~"Confirm",
                                       TRUE~"Reject")) %>% 
  select(-Z0,-Z1,-Z2,-PI_HAT) %>% 
  inner_join(ped2check_genome %>% 
               rename(FullSampleName=IID1,SireID=IID2) %>% 
               bind_rows(ped2check_genome %>% 
                           rename(FullSampleName=IID2,SireID=IID1))) %>% 
  distinct %>% 
  mutate(ConfirmMaleParent=case_when(Z0<0.32 & Z1>0.67~"Confirm",
                                       SireID==DamID & PI_HAT>0.6 & Z0<0.3 & Z2>0.32~"Confirm",
                                       TRUE~"Reject")) %>% 
  select(-Z0,-Z1,-Z2,-PI_HAT)

ped2check %>% 
  count(ConfirmFemaleParent,ConfirmMaleParent) %>% mutate(Prop=round(n/sum(n),2))

  ConfirmFemaleParent ConfirmMaleParent    n Prop
1             Confirm           Confirm 4473 0.72
2             Confirm            Reject  715 0.12
3              Reject           Confirm  442 0.07
4              Reject            Reject  576 0.09

ped2check %>% 
  mutate(Cohort=NA,
         Cohort=ifelse(grepl("TMS20",FullSampleName,ignore.case = T),"TMS20",
                       ifelse(grepl("TMS19",FullSampleName,ignore.case = T),"TMS19",
                              ifelse(grepl("TMS18",FullSampleName,ignore.case = T),"TMS18",
                                     ifelse(grepl("TMS17",FullSampleName,ignore.case = T),"TMS17",
                                            ifelse(grepl("TMS16",FullSampleName,ignore.case = T),"TMS16",
                                                   ifelse(grepl("TMS15",FullSampleName,ignore.case = T),"TMS15",
                                                          ifelse(grepl("TMS14",FullSampleName,ignore.case = T),"TMS14",
                                                                 ifelse(grepl("TMS13|2013_",FullSampleName,
                                                                              ignore.case = T),"TMS13","GGetc"))))))))) %>% 
  filter(ConfirmFemaleParent=="Confirm",
         ConfirmMaleParent=="Confirm") %>% 
  count(Cohort,name = "BothParentsConfirmed")

  Cohort BothParentsConfirmed
1  GGetc                   20
2  TMS13                 1786
3  TMS14                 1303
4  TMS15                  589
5  TMS17                   11
6  TMS18                  592
7  TMS19                   40
8  TMS20                  132

I’m only interested in families / trios that are confirmed. Remove any without both parents confirmed.

correctedped<-ped2check %>% 
  filter(ConfirmFemaleParent=="Confirm",
         ConfirmMaleParent=="Confirm") %>% 
  select(-contains("Confirm"))

correctedped %>% 
  count(SireID,DamID) %>% arrange(desc(n))

                       SireID                     DamID  n
1           I020129:250090842         I011412:250300323 77
2          MM990477:250090809         I011412:250300323 48
3           I970290:250090804         I940237:250164036 46
4           I011797:250090770         I070004:250164022 45
5           TMEB117:250253666         I961632:250300546 45
6           I940006:250090826         I030075:250300232 41
7           I980002:250300438          I30572:250253643 40
8           I930007:250090827         I970425:250300465 39
9           I980510:250303662         I980505:250090767 38
10          I071313:250164024         I011412:250300323 37
11          TMEB419:250253865         TMEB419:250253865 35
12          I020233:250300288         I011412:250300323 33
13           I30572:250253643         I980505:250090767 31
14          I010046:250300307         I940237:250164036 30
15          I020540:250300283         I011412:250300323 29
16          I970290:250090804         I950306:250164034 28
17          I930007:250090827         I071313:250164024 26
18          I011412:250300323         I070004:250164022 25
19          I940006:250090826        B9200068:250304480 25
20          M940583:250164037         I010046:250300307 25
21          M980068:250300452        MM964500:250300562 24
22          I010903:250300322         I030060:250090848 23
23          I930007:250090827         I974766:250300468 23
24          TMEB778:250254008         TMEB693:250253991 22
25          I930007:250090827         I000211:250300361 21
26          I940006:250090826        MM964500:250300562 21
27          TMEB419:250253865         I020285:250300276 21
28          I010903:250300322         I970353:250090805 20
29          I980581:250253626         I980002:250300438 20
30          I010903:250300322         I020129:250090842 19
31          I071313:250164024         I970290:250090804 19
32          I950279:250164033         I063046:250300177 19
33          I980002:250300438         I020285:250300276 19
34          I000355:250300360         I020129:250090842 18
35          I010903:250300322         I972205:250301855 18
36          I030075:250300232         I010046:250300307 18
37          I980581:250253626          I30572:250253643 18
38         MM970646:250300486         I030060:250090848 18
39          I960963:250300550         I070258:250300140 17
40          I972205:250301855    2013_0343_22:250162550 17
41         MM970806:250164028         I011412:250300323 17
42     2013_0307_20:250161028    2013_10084_6:250164723 16
43          I010046:250300307         M940583:250164037 16
44          I020129:250090842         TMEB419:250253865 16
45          I071313:250164024         I970353:250090805 16
46          I972205:250301855     2013_0088_7:250159759 16
47          I980581:250253626         Z930151:250164040 16
48      2013_0008_6:250162074    2013_0336_23:250162476 15
49    2013_10063_19:250164239    2013_0307_10:250160606 15
50    2013_10063_19:250164239    2013_10084_6:250164723 15
51          I000070:250300358         I961632:250300546 15
52          I000211:250300361         I930134:250164039 15
53         I030055A:250300218         I020540:250300283 15
54          I030075:250300232         I020129:250090842 15
55          I071313:250164024         I020285:250300276 15
56          I930007:250090827         I972205:250301855 15
57          I930134:250164039         Z930151:250164040 15
58          Z930151:250164040        MM970806:250164028 15
59      2013_0108_7:250159843     2013_0307_8:250160604 14
60      2013_0333_3:250162424    2013_10020_4:250164717 14
61          I011371:250090769         I020431:250300292 14
62          I020129:250090842         M980004:250164026 14
63         I030060A:250300227    2013_0053_10:250162218 14
64          I071313:250164024        MM970806:250164028 14
65          I930007:250090827     2013_0088_7:250159759 14
66          I970290:250090804        MM970016:250164029 14
67         MM970043:250300482        I030055A:250300218 14
68         MM970043:250300482         I993073:250300423 14
69         MM970043:250300482        MM964500:250300562 14
70         MM970043:250300482         Z930151:250164040 14
71          TMEB419:250253865         I940237:250164036 14
72      2013_0088_7:250159759    2013_0053_15:250162223 13
73     2013_0111_12:250160049     2013_0307_8:250160604 13
74          I000211:250300361        B9200068:250304480 13
75          I930007:250090827         I020285:250300276 13
76          I940006:250090826         I000345:250090783 13
77          I950279:250164033         I070126:250164023 13
78          I972205:250301855    2013_0053_15:250162223 13
79          I972205:250301855     2013_0343_2:250162499 13
80          I972205:250301855        B9200068:250304480 13
81          I974766:250300468         I980196:250164025 13
82         MM970043:250300482         I030060:250090848 13
83  TMS13F1106P0006:250300932     2013_0423_9:250162755 13
84      2013_0108_7:250159843    2013_0307_20:250161028 12
85      2013_0214_4:250160658   2013_10063_19:250164239 12
86     2013_0307_20:250161028    2013_0153_11:250160352 12
87      2013_0307_7:250160603    2013_10309_1:250164479 12
88      2013_0333_3:250162424    2013_0153_11:250160352 12
89          I010046:250300307         I980002:250300438 12
90          I020129:250090842         I950971:250300591 12
91          I020285:250300276         I980002:250300438 12
92         I030055A:250300218         I961632:250300546 12
93          I051553:250300205         I070004:250164022 12
94          I920429:250164041        B9200061:250304482 12
95          I930007:250090827    2013_0307_16:250160612 12
96          I930134:250164039         I020540:250300283 12
97          I930134:250164039         I070258:250300140 12
98          I940006:250090826         I000211:250300361 12
99          I950306:250164034         I950971:250300591 12
100         I971228:250164027         I011412:250300323 12
101         M980004:250164026         I950971:250300591 12
102        MM970806:250164028         I030060:250090848 12
103        MM990268:250300436         I011412:250300323 12
104         TMEB419:250253865         I972205:250301855 12
105         TMEB419:250253865         I974766:250300468 12
106     2013_0008_6:250162074     2013_0087_2:250159576 11
107     2013_0108_7:250159843    2013_0107_10:250159835 11
108     2013_0108_7:250159843     2013_0436_5:250162760 11
109     2013_0212_2:250159907    2013_10120_1:250164341 11
110    2013_0212_32:250159937     2013_0423_9:250162755 11
111     2013_0307_8:250160604     2013_0212_2:250159907 11
112     2013_0307_8:250160604    2013_10020_4:250164717 11
113     2013_0333_3:250162424     2013_0024_2:250162894 11
114    2013_10059_6:250164095     2013_0436_5:250162760 11
115         I000070:250300358    2013_0053_10:250162218 11
116         I010046:250300307         I010903:250300322 11
117         I010903:250300322         I000211:250300361 11
118        I030055A:250300218         I020431:250300292 11
119         I930007:250090827         I940018:250164035 11
120         I940006:250090826         I000214:250300403 11
121         M980004:250164026         I971228:250164027 11
122         M980068:250300452         I930265:250164038 11
123        MM970043:250300482         I020431:250300292 11
124        MM970806:250164028         I993073:250300423 11
125 TMS13F1106P0006:250300932     2013_0088_8:250159760 11
126         Z930151:250164040         I020540:250300283 11
127     2013_0108_7:250159843     2013_0333_3:250162424 10
128     2013_0108_7:250159843    2013_10084_6:250164723 10
129     2013_0212_2:250159907    2013_0332_42:250161115 10
130     2013_0212_2:250159907    2013_10063_7:250164227 10
131    2013_0212_32:250159937     2013_0436_5:250162760 10
132    2013_0333_17:250162439    2013_0153_11:250160352 10
133    2013_0333_17:250162439 TMS13F1391P0039:250465621 10
134     2013_0333_3:250162424     2013_0160_3:250160398 10
135     2013_0333_3:250162424    2013_0212_55:250159960 10
136     2013_0436_4:250162759   2013_10063_19:250164239 10
137   2013_10063_19:250164239    2013_10303_2:250164467 10
138   2013_10069_24:250164153    2013_0307_16:250160612 10
139    2013_10303_3:250164468     2013_0381_5:250162690 10
140         I010046:250300307         I070004:250164022 10
141         I020285:250300276         I010903:250300322 10
142        I030055A:250300218        MM970806:250164028 10
143        I030060A:250300227    2013_0343_22:250162550 10
144         I051740:250300206         I993073:250300423 10
145         I970425:250300465         I993073:250300423 10
146         M980068:250300452         I010903:250300322 10
147         M980068:250300452         I011412:250300323 10
148 TMS14F1292P0015:250304248 TMS14F1229P0002:250303379 10
149         Z930151:250164040         I980196:250164025 10
150     2013_0088_7:250159759    2013_0307_16:250160612  9
151     2013_0108_7:250159843    2013_10306_3:250164474  9
152    2013_0212_32:250159937     2013_0050_8:250169056  9
153    2013_0212_32:250159937     2013_0333_3:250162424  9
154    2013_0212_32:250159937    2013_0336_23:250162476  9
155    2013_0212_55:250159960     2013_0154_8:250160392  9
156    2013_0333_17:250162439    2013_10020_4:250164717  9
157    2013_10303_1:250164466    2013_10122_3:250164747  9
158         I020129:250090842         I930007:250090827  9
159        I030060A:250300227     2013_0343_2:250162499  9
160         I930007:250090827    2013_10020_1:250164714  9
161         I930007:250090827         I070004:250164022  9
162         I930007:250090827         I970290:250090804  9
163         I940006:250090826         I993073:250300423  9
164         I972205:250301855    2013_0053_10:250162218  9
165          KALESO:250304590         I000211:250300361  9
166          KALESO:250304590         I011412:250300323  9
167        MM970806:250164028         I020431:250300292  9
168        MM970806:250164028        I030055A:250300218  9
169        MM970806:250164028         I930007:250090827  9
170         TMEB419:250253865          I30572:250253643  9
171 TMS13F1106P0006:250300932    2013_10063_9:250164229  9
172     2013_0212_2:250159907    2013_10084_6:250164723  8
173    2013_0307_20:250161028     2013_0109_9:250160030  8
174     2013_0307_4:250160600     2013_0381_5:250162690  8
175     2013_0307_4:250160600    2013_10084_6:250164723  8
176     2013_0307_8:250160604    2013_0333_27:250162449  8
177     2013_0333_3:250162424     2013_0212_2:250159907  8
178     2013_0436_4:250162759     2013_0307_4:250160600  8
179    2013_10020_2:250164715    2013_0307_20:250161028  8
180    2013_10059_6:250164095     2013_0107_6:250159831  8
181         I000211:250300361         I020129:250090842  8
182        I030060A:250300227    2013_0053_15:250162223  8
183         I030075:250300232         I030007:250300231  8
184         I920429:250164041         I930134:250164039  8
185         I930007:250090827     2013_0343_2:250162499  8
186         I930007:250090827         I960860:250164032  8
187         I930007:250090827         I971228:250164027  8
188         I930007:250090827         I974580:250300467  8
189         I930134:250164039         I993073:250300423  8
190         I950279:250164033         I960860:250164032  8
191         TMEB419:250253865     2013_0343_2:250162499  8
192 TMS13F1106P0006:250300932    2013_0008_20:250162088  8
193 TMS13F1106P0006:250300932    2013_0212_55:250159960  8
194 TMS14F1157P0002:250301832 TMS14F1243P0019:250303486  8
195 TMS14F1234P0001:250303393         TMEB693:250253991  8
196         Z930151:250164040         I020131:250300295  8
197         Z930151:250164040         I930134:250164039  8
198     2013_0079_2:250159538   2013_10063_19:250164239  7
199     2013_0108_7:250159843     2013_0028_7:250162328  7
200     2013_0108_7:250159843     2013_0088_8:250159760  7
201     2013_0108_7:250159843    2013_0333_14:250162435  7
202    2013_0154_10:250160394    2013_0212_32:250159937  7
203    2013_0154_10:250160394    2013_0212_58:250159963  7
204     2013_0212_2:250159907    2013_0045_19:250169030  7
205     2013_0212_2:250159907     2013_0079_7:250159543  7
206     2013_0212_2:250159907     2013_0423_9:250162755  7
207    2013_0212_32:250159937    2013_0436_12:250162767  7
208    2013_0307_20:250161028    2013_0107_10:250159835  7
209    2013_0307_20:250161028 TMS13F1106P0006:250300932  7
210    2013_0333_27:250162449     2013_0212_2:250159907  7
211     2013_0333_3:250162424    2013_0212_32:250159937  7
212     2013_0333_3:250162424     2013_0214_4:250160658  7
213   2013_10063_19:250164239     2013_0307_6:250160602  7
214   2013_10063_19:250164239     2013_0381_5:250162690  7
215    2013_10309_1:250164479   2013_10063_19:250164239  7
216         I000070:250300358     2013_0160_5:250160400  7
217         I071313:250164024         I950971:250300591  7
218          I30572:250253643         TMEB419:250253865  7
219         I930007:250090827    2013_0343_22:250162550  7
220         I930007:250090827         I070593:250300163  7
221         I972205:250301855    2013_10020_1:250164714  7
222        MM990268:250300436         I000211:250300361  7
223         TMEB419:250253865    2013_0053_10:250162218  7
224         TMEB419:250253865    2013_10020_1:250164714  7
225 TMS14F1085P0003:250303128 TMS14F1213P0002:250302239  7
226 TMS14F1240P0005:250303462 TMS14F1283P0002:250303981  7
227 TMS15F1318P0024:250476735 TMS15F1080P0004:250465178  7
228     2013_0008_6:250162074    2013_10086_3:250164329  6
229    2013_0053_15:250162223    2013_0307_16:250160612  6
230     2013_0079_2:250159538    2013_0307_10:250160606  6
231     2013_0108_7:250159843 TMS13F1106P0006:250300932  6
232    2013_0154_10:250160394    2013_0212_79:250160650  6
233    2013_0212_32:250159937     2013_0109_9:250160030  6
234    2013_0212_55:250159960    2013_0153_11:250160352  6
235    2013_0216_10:250160702     2013_0423_9:250162755  6
236    2013_0307_20:250161028    2013_0333_17:250162439  6
237    2013_0307_20:250161028     2013_0333_3:250162424  6
238    2013_0333_17:250162439    2013_0045_19:250169030  6
239     2013_0333_2:250162423    2013_0153_11:250160352  6
240     2013_0333_3:250162424     2013_0028_7:250162328  6
241     2013_0333_3:250162424    2013_0212_79:250160650  6
242     2013_0333_3:250162424    2013_10309_1:250164479  6
243    2013_10084_6:250164723     2013_0307_8:250160604  6
244    2013_10122_3:250164747   2013_10063_19:250164239  6
245         I000355:250300360         I030060:250090848  6
246         I011797:250090770         I011368:250300318  6
247         I020129:250090842        MM964500:250300562  6
248         I051740:250300206         I000211:250300361  6
249         I930007:250090827    2013_0053_10:250162218  6
250         I930265:250164038         I030060:250090848  6
251         I940006:250090826         I960869:250300548  6
252         I972205:250301855    2013_0307_16:250160612  6
253         I972205:250301855         I070593:250300163  6
254          KALESO:250304590         I996069:250300420  6
255         TMEB419:250253865    2013_0307_16:250160612  6
256    TMS13F1227P0119_A19491 TMS14F1284P0001:250304001  6
257 TMS13F1300P0075:250465619     2013_0079_7:250159543  6
258 TMS14F1085P0003:250303128 TMS14F1196P0005:250302110  6
259 TMS14F1176P0006:250301993 TMS14F1174P0011:250301981  6
260 TMS15F1021P0028:250464932 TMS15F1329P0005:250476750  6
261 TMS15F1069P0007:250521086 TMS15F1351P0003:250466280  6
262 TMS15F1132P0013:250475590 TMS15F1153P0009:250465409  6
263     2013_0008_6:250162074     2013_0154_8:250160392  5
264     2013_0008_6:250162074     2013_0333_2:250162423  5
265     2013_0079_2:250159538     2013_0307_6:250160602  5
266     2013_0088_7:250159759    2013_0343_22:250162550  5
267     2013_0108_7:250159843     2013_0107_6:250159831  5
268    2013_0111_12:250160049    2013_10063_9:250164229  5
269    2013_0154_10:250160394     2013_0212_2:250159907  5
270    2013_0154_10:250160394    2013_0333_14:250162435  5
271     2013_0212_2:250159907     2013_0079_5:250159541  5
272     2013_0212_2:250159907     2013_0333_2:250162423  5
273     2013_0212_2:250159907     2013_0333_3:250162424  5
274    2013_0212_32:250159937    2013_10120_1:250164341  5
275    2013_0212_55:250159960    2013_10084_6:250164723  5
276     2013_0212_7:250159912   2013_10063_19:250164239  5
277    2013_0214_14:250160668    2013_0008_20:250162088  5
278    2013_0307_20:250161028    2013_0212_55:250159960  5
279    2013_0307_20:250161028 TMS13F1391P0039:250465621  5
280     2013_0307_4:250160600    2013_0214_14:250160668  5
281     2013_0307_8:250160604    2013_0332_42:250161115  5
282     2013_0333_3:250162424     2013_0087_2:250159576  5
283     2013_0333_3:250162424    2013_0332_42:250161115  5
284    2013_10020_2:250164715 TMS13F1106P0006:250300932  5
285   2013_10063_19:250164239    2013_10124_2:250164352  5
286    2013_10303_1:250164466     2013_0381_5:250162690  5
287    2013_10303_2:250164467     2013_0381_5:250162690  5
288    2013_10303_2:250164467    2013_10084_6:250164723  5
289    2013_10303_3:250164468    2013_10084_6:250164723  5
290         I000070:250300358    2013_0343_22:250162550  5
291         I000203:250300407          I30572:250253643  5
292         I000350:250300359         I070004:250164022  5
293         I020129:250090842         I971149:250300466  5
294         I970425:250300465         I010903:250300322  5
295         I972205:250301855    2013_10122_5:250164749  5
296         M940583:250164037         I030060:250090848  5
297         M980068:250300452         I996016:250090791  5
298         TMEB419:250253865     2013_0088_7:250159759  5
299         TMEB419:250253865        MM965280:250300556  5
300 TMS14F1085P0003:250303128 TMS14F1213P0007:250302244  5
301 TMS14F1113P0002:250301450 TMS14F1283P0008:250303987  5
302 TMS14F1138P0005:250301674 TMS14F1240P0005:250303462  5
303 TMS14F1138P0005:250301674 TMS14F1244P0006:250303493  5
304 TMS14F1241P0002:250303465 TMS14F1213P0007:250302244  5
305 TMS14F1284P0001:250304001     2013_0160_5:250160400  5
306 TMS15F1153P0009:250465409 TMS15F1092P0016:250465193  5
307 TMS15F1177P0004:250476294 TMS15F1154P0002:250518934  5
308 TMS15F1398P0008:250466574 TMS15F1079P0025:250465175  5
309         Z930151:250164040         I030060:250090848  5
310     2013_0008_6:250162074    2013_10124_2:250164352  4
311     2013_0079_2:250159538     2013_0307_4:250160600  4
312     2013_0108_7:250159843    2013_0307_11:250160607  4
313    2013_0154_10:250160394     2013_0107_8:250159833  4
314    2013_0154_10:250160394    2013_0202_46:250160176  4
315    2013_0154_10:250160394    2013_0216_26:250160718  4
316     2013_0212_2:250159907   2013_10145_11:250164626  4
317    2013_0212_32:250159937     2013_0107_6:250159831  4
318    2013_0212_32:250159937    2013_0111_12:250160049  4
319    2013_0212_32:250159937    2013_0153_11:250160352  4
320    2013_0212_55:250159960     2013_0381_5:250162690  4
321    2013_0212_55:250159960     2013_0420_6:250162738  4
322     2013_0212_7:250159912    2013_10084_6:250164723  4
323    2013_0214_29:250160683     2013_0107_8:250159833  4
324    2013_0214_29:250160683    2013_0307_20:250161028  4
325    2013_0216_10:250160702     2013_0324_2:250161035  4
326    2013_0307_11:250160607    2013_10122_3:250164747  4
327    2013_0307_20:250161028     2013_0324_2:250161035  4
328     2013_0307_8:250160604     2013_0088_8:250159760  4
329     2013_0307_8:250160604    2013_0212_55:250159960  4
330    2013_0332_27:250161100    2013_10122_3:250164747  4
331    2013_0333_17:250162439    2013_0332_42:250161115  4
332    2013_0333_17:250162439    2013_0336_23:250162476  4
333    2013_0333_17:250162439    2013_10084_6:250164723  4
334     2013_0333_3:250162424     2013_0108_7:250159843  4
335    2013_10020_2:250164715    2013_10303_1:250164466  4
336    2013_10084_6:250164723     2013_0212_2:250159907  4
337    2013_10084_6:250164723    2013_0212_79:250160650  4
338    2013_10122_3:250164747     2013_0381_5:250162690  4
339    2013_10303_2:250164467    2013_10124_2:250164352  4
340    2013_10306_3:250164474    2013_0008_20:250162088  4
341        I030060A:250300227         I090516:250099187  4
342         I071378:250300142         I950986:250300582  4
343         I974766:250300468         I940018:250164035  4
344         I980002:250300438         I030075:250300232  4
345 TMS13F1106P0006:250300932     2013_0212_2:250159907  4
346 TMS13F1106P0006:250300932    2013_0212_79:250160650  4
347 TMS13F1106P0006:250300932    2013_0307_20:250161028  4
348 TMS14F1091P0008:250303196 TMS14F1229P0004:250303381  4
349 TMS14F1113P0002:250301450 TMS14F1174P0011:250301981  4
350 TMS14F1138P0005:250301674 TMS14F1122P0003:250301540  4
351 TMS14F1138P0005:250301674 TMS14F1189P0001:250302072  4
352 TMS14F1138P0005:250301674 TMS14F1283P0002:250303981  4
353 TMS14F1166P0002:250301867 TMS14F1154P0001:250301818  4
354 TMS14F1166P0002:250301867 TMS14F1284P0001:250304001  4
355 TMS14F1176P0006:250301993 TMS14F1085P0003:250303128  4
356 TMS14F1240P0005:250303462 TMS14F1138P0005:250301674  4
357 TMS14F1284P0001:250304001 TMS14F1201P0003:250302135  4
358 TMS14F1300P0002:250300902    TMS15F1467P0011_A19549  4
359 TMS15F1021P0028:250464932 TMS15F1159P0006:250465430  4
360 TMS15F1132P0013:250475590 TMS15F1244P0004:250465827  4
361 TMS15F1132P0013:250475590 TMS15F1300P0002:250476689  4
362 TMS15F1177P0004:250476294 TMS15F1130P0007:250465327  4
363 TMS15F1310P0019:250467021 TMS15F1024P0006:250464990  4
364 TMS15F1326P0004:250467063 TMS15F1072P0006:250521114  4
365 TMS15F1367P0001:250475193 TMS15F1124P0001:250465316  4
366 TMS15F1398P0008:250466574 TMS15F1072P0012:250521118  4
367     2013_0050_8:250169056    2013_0307_11:250160607  3
368     2013_0079_2:250159538     2013_0212_7:250159912  3
369     2013_0079_2:250159538    2013_10303_1:250164466  3
370     2013_0108_7:250159843     2013_0087_2:250159576  3
371    2013_0111_12:250160049    2013_0212_55:250159960  3
372     2013_0212_2:250159907     2013_0160_9:250160405  3
373     2013_0212_2:250159907    2013_0333_14:250162435  3
374    2013_0212_32:250159937     2013_0160_9:250160405  3
375    2013_0212_32:250159937    2013_0332_45:250161118  3
376    2013_0212_32:250159937 TMS13F1391P0039:250465621  3
377    2013_0212_55:250159960    2013_10020_4:250164717  3
378    2013_0212_55:250159960    2013_10063_9:250164229  3
379    2013_0212_55:250159960 TMS13F1106P0006:250300932  3
380     2013_0212_7:250159912    2013_10122_3:250164747  3
381    2013_0216_10:250160702     2013_0088_8:250159760  3
382     2013_0307_4:250160600    2013_0332_27:250161100  3
383     2013_0307_4:250160600    2013_10122_3:250164747  3
384     2013_0307_8:250160604    2013_10020_2:250164715  3
385     2013_0307_8:250160604    2013_10063_9:250164229  3
386     2013_0307_8:250160604   2013_10145_23:250164638  3
387    2013_0332_27:250161100    2013_0307_11:250160607  3
388     2013_0333_2:250162423    2013_10020_2:250164715  3
389     2013_0333_3:250162424     2013_0154_8:250160392  3
390     2013_0343_2:250162499    2013_0307_16:250160612  3
391    2013_0343_22:250162550    TMS15F1467P0033_A19532  3
392     2013_0381_5:250162690     2013_0307_4:250160600  3
393     2013_0381_5:250162690   2013_10063_19:250164239  3
394    2013_10020_2:250164715     2013_0107_6:250159831  3
395    2013_10020_2:250164715    2013_0212_79:250160650  3
396    2013_10059_6:250164095     2013_0107_8:250159833  3
397   2013_10063_19:250164239     2013_0050_8:250169056  3
398   2013_10063_19:250164239    2013_10303_3:250164468  3
399    2013_10084_6:250164723    2013_0307_20:250161028  3
400    2013_10084_6:250164723     2013_0307_4:250160600  3
401    2013_10122_3:250164747    2013_10084_6:250164723  3
402    2013_10303_1:250164466     2013_0050_8:250169056  3
403         I000017:250300396         I070258:250300140  3
404         I000070:250300358    2013_0307_16:250160612  3
405         I011797:250090770         I974580:250300467  3
406         I020129:250090842         Z930151:250164040  3
407         I020540:250300283         I930265:250164038  3
408          I30572:250253643         I980002:250300438  3
409         I930134:250164039        MM990268:250300436  3
410         I950306:250164034        MM990477:250090809  3
411         I960023:250164030         I020431:250300292  3
412        MM990268:250300436         I971228:250164027  3
413         TMEB419:250253865    2013_0053_15:250162223  3
414         TMEB419:250253865     2013_0160_5:250160400  3
415         TMEB419:250253865         I980505:250090767  3
416         TMEB693:250253991         I090516:250099187  3
417 TMS13F1106P0006:250300932     2013_0307_8:250160604  3
418 TMS14F1085P0003:250303128 TMS14F1196P0001:250302106  3
419 TMS14F1113P0002:250301450 TMS14F1091P0009:250303197  3
420 TMS14F1174P0011:250301981 TMS14F1283P0013:250303992  3
421 TMS14F1176P0010:250301997 TMS14F1283P0002:250303981  3
422 TMS14F1195P0008:250302099 TMS14F1107P0004:250301360  3
423 TMS14F1233P0003:250303390 TMS14F1284P0001:250304001  3
424 TMS14F1240P0005:250303462 TMS14F1153P0003:250301810  3
425 TMS14F1240P0005:250303462 TMS14F1283P0008:250303987  3
426 TMS14F1255P0005:250303597     2013_0053_2:250162210  3
427 TMS14F1284P0001:250304001 TMS14F1244P0006:250303493  3
428 TMS14F1292P0010:250304243 TMS14F1154P0001:250301818  3
429 TMS15F1153P0009:250465409 TMS15F1100P0005:250465254  3
430 TMS15F1177P0004:250476294 TMS15F1130P0012:250475583  3
431 TMS15F1177P0004:250476294 TMS15F1132P0013:250475590  3
432 TMS15F1305P0021:250476698 TMS15F1025P0001:250464993  3
433 TMS15F1351P0003:250466280 TMS15F1124P0001:250465316  3
434 TMS15F1396P0004:250466562 TMS15F1153P0009:250465409  3
435     2013_0008_6:250162074     2013_0028_7:250162328  2
436     2013_0008_6:250162074     2013_0109_9:250160030  2
437     2013_0008_6:250162074    2013_0214_14:250160668  2
438     2013_0008_6:250162074     2013_0307_4:250160600  2
439    2013_0053_15:250162223    2013_0053_10:250162218  2
440    2013_0053_15:250162223     2013_0160_5:250160400  2
441     2013_0079_2:250159538    2013_10303_2:250164467  2
442     2013_0088_8:250159760    2013_10122_3:250164747  2
443     2013_0108_7:250159843     2013_0079_2:250159538  2
444     2013_0108_7:250159843    2013_0332_42:250161115  2
445    2013_0111_12:250160049     2013_0307_4:250160600  2
446    2013_0111_12:250160049    2013_10306_3:250164474  2
447     2013_0153_7:250160348     2013_0107_8:250159833  2
448    2013_0154_10:250160394    2013_0212_55:250159960  2
449    2013_0154_10:250160394     2013_0333_2:250162423  2
450    2013_0154_10:250160394    2013_0333_27:250162449  2
451     2013_0212_2:250159907   2013_10034_19:250164218  2
452    2013_0212_32:250159937     2013_0024_2:250162894  2
453    2013_0212_32:250159937    2013_0045_19:250169030  2
454    2013_0212_32:250159937     2013_0333_2:250162423  2
455    2013_0212_32:250159937    2013_10020_4:250164717  2
456    2013_0212_32:250159937 TMS13F1101P0007:250301198  2
457     2013_0212_7:250159912     2013_0050_8:250169056  2
458     2013_0212_7:250159912    2013_0087_14:250159588  2
459    2013_0216_10:250160702    2013_0333_17:250162439  2
460    2013_0216_10:250160702     2013_0436_6:250162761  2
461     2013_0216_6:250160698     2013_0107_4:250159829  2
462    2013_0307_11:250160607   2013_10063_19:250164239  2
463    2013_0307_11:250160607    2013_10084_6:250164723  2
464    2013_0307_16:250160612    2013_0053_10:250162218  2
465    2013_0307_20:250161028     2013_0024_2:250162894  2
466    2013_0307_20:250161028     2013_0028_7:250162328  2
467    2013_0307_20:250161028     2013_0079_7:250159543  2
468    2013_0307_20:250161028    2013_0336_23:250162476  2
469    2013_0307_20:250161028 TMS13F1101P0007:250301198  2
470     2013_0307_4:250160600     2013_0050_8:250169056  2
471     2013_0307_6:250160602   2013_10063_19:250164239  2
472     2013_0307_6:250160602    2013_10084_6:250164723  2
473     2013_0307_7:250160603        I030060A:250300227  2
474     2013_0307_8:250160604    2013_0214_14:250160668  2
475    2013_0333_10:250162431     2013_0307_7:250160603  2
476    2013_0333_27:250162449    2013_10122_3:250164747  2
477     2013_0333_3:250162424     2013_0153_7:250160348  2
478     2013_0333_3:250162424     2013_0154_5:250160358  2
479    2013_0343_22:250162550     2013_0160_5:250160400  2
480    2013_0343_44:250162573     2013_0307_4:250160600  2
481    2013_0343_44:250162573 TMS14F1255P0005:250303597  2
482    2013_0343_44:250162573 TMS14F1284P0001:250304001  2
483     2013_0436_4:250162759     2013_0160_3:250160398  2
484   2013_10063_19:250164239    2013_0307_11:250160607  2
485   2013_10063_19:250164239     2013_0307_4:250160600  2
486   2013_10063_19:250164239    2013_0332_27:250161100  2
487   2013_10063_19:250164239     2013_0436_4:250162759  2
488   2013_10069_24:250164153    2013_0343_22:250162550  2
489    2013_10084_3:250164720    2013_0214_14:250160668  2
490    2013_10084_6:250164723    2013_10303_1:250164466  2
491    2013_10122_5:250164749    2013_10020_1:250164714  2
492    2013_10303_1:250164466     2013_0436_4:250162759  2
493    2013_10303_1:250164466    2013_10084_6:250164723  2
494    2013_10303_2:250164467     2013_0214_4:250160658  2
495    2013_10303_2:250164467   2013_10063_19:250164239  2
496    2013_10303_2:250164467    2013_10309_1:250164479  2
497    2013_10303_3:250164468    2013_10124_2:250164352  2
498         I000070:250300358 TMS14F1201P0003:250302135  2
499         I000070:250300358 TMS15F1130P0012:250475583  2
500         I000203:250300407         I940018:250164035  2
501         I011368:250300318         I070593:250300163  2
502         I011797:250090770         I070593:250300163  2
503        I030055A:250300218         I930265:250164038  2
504         I030060:250090848    2013_0053_10:250162218  2
505         I070004:250164022        MM990268:250300436  2
506         I930007:250090827   2013_10063_13:250164233  2
507         I930007:250090827         I011412:250300323  2
508         I930007:250090827         I090516:250099187  2
509         I940263:250300608         I940561:250090825  2
510        I961089A:250300537        I961089A:250300537  2
511         I972205:250301855         I011797:250090770  2
512         I972205:250301855 TMS15F1021P0013:250464921  2
513           TMEB1:250253593          I91934:250304625  2
514         TMEB419:250253865    2013_0343_22:250162550  2
515         TMEB419:250253865 TMS14F1016P0006:250302439  2
516         TMEB419:250253865 TMS14F1284P0001:250304001  2
517           TMEB7:250253599     2013_0160_5:250160400  2
518 TMS13F1106P0006:250300932    2013_0212_58:250159963  2
519 TMS14F1035P0004:250302641 TMS14F1016P0006:250302439  2
520 TMS14F1063P0003:250302894 TMS14F1154P0001:250301818  2
521 TMS14F1113P0002:250301450 TMS14F1213P0007:250302244  2
522 TMS14F1157P0002:250301832 TMS14F1189P0001:250302072  2
523 TMS14F1166P0002:250301867 TMS14F1107P0004:250301360  2
524 TMS14F1166P0002:250301867 TMS14F1169P0001:250301880  2
525 TMS14F1174P0011:250301981 TMS14F1153P0003:250301810  2
526 TMS14F1174P0011:250301981 TMS14F1229P0004:250303381  2
527 TMS14F1174P0011:250301981 TMS14F1283P0002:250303981  2
528 TMS14F1176P0006:250301993 TMS14F1091P0008:250303196  2
529 TMS14F1176P0006:250301993 TMS14F1138P0005:250301674  2
530 TMS14F1176P0006:250301993 TMS14F1222P0003:250303322  2
531 TMS14F1240P0004:250303461 TMS14F1283P0015:250303994  2
532 TMS14F1240P0005:250303462 TMS14F1174P0011:250301981  2
533 TMS14F1240P0005:250303462 TMS14F1276P0005:250303833  2
534 TMS14F1240P0005:250303462 TMS14F1283P0013:250303992  2
535 TMS14F1241P0002:250303465 TMS14F1107P0004:250301360  2
536 TMS14F1247P0007:250303518 TMS14F1229P0004:250303381  2
537 TMS14F1288P0001:250304117 TMS14F1091P0009:250303197  2
538 TMS14F1292P0010:250304243 TMS14F1154P0002:250301819  2
539 TMS15F1069P0007:250521086 TMS15F1333P0001:250467074  2
540 TMS15F1132P0013:250475590 TMS15F1100P0005:250465254  2
541 TMS15F1132P0013:250475590 TMS15F1154P0015:250518942  2
542 TMS15F1132P0013:250475590 TMS15F1234P0001:250465795  2
543 TMS15F1153P0009:250465409 TMS15F1109P0003:250465275  2
544 TMS15F1153P0009:250465409 TMS15F1130P0012:250475583  2
545 TMS15F1156P0014:250518954 TMS15F1072P0031:250521122  2
546 TMS15F1156P0014:250518954 TMS15F1080P0004:250465178  2
547 TMS15F1156P0014:250518954 TMS15F1104P0001:250465265  2
548 TMS15F1156P0014:250518954 TMS15F1109P0003:250465275  2
549 TMS15F1159P0001:250518960 TMS15F1276P0003:250465968  2
550 TMS15F1159P0001:250518960 TMS15F1324P0004:250476746  2
551 TMS15F1159P0001:250518960 TMS15F1326P0004:250467063  2
552 TMS15F1177P0004:250476294 TMS15F1132P0001:250465369  2
553 TMS15F1195P0009:250465561 TMS15F1103P0006:250465263  2
554 TMS15F1318P0009:250476726 TMS15F1103P0006:250465263  2
555 TMS15F1326P0004:250467063 TMS15F1160P0010:250518971  2
556 TMS15F1367P0001:250475193 TMS15F1326P0004:250467063  2
557 TMS15F1396P0004:250466562 TMS15F1130P0012:250475583  2
558 TMS15F1397P0001:250466568 TMS15F1103P0006:250465263  2
559 TMS15F1398P0008:250466574 TMS15F1124P0001:250465316  2
560 TMS15F1398P0008:250466574 TMS15F1130P0002:250475578  2
561    TMS18F1092P0022_A18764    TMS18F1015P0015_A18729  2
562    TMS18F1173P0009_A18858    TMS18F1026P0014_A18745  2
563    TMS18F1173P0009_A18858    TMS18F1047P0024_A18757  2
564    2013_0003_16:250162068     2013_0050_8:250169056  1
565     2013_0003_3:250162055    2013_0343_26:250162554  1
566     2013_0008_6:250162074     2013_0079_7:250159543  1
567     2013_0008_6:250162074    2013_0111_12:250160049  1
568     2013_0008_6:250162074     2013_0160_3:250160398  1
569     2013_0008_6:250162074     2013_0212_2:250159907  1
570     2013_0008_6:250162074    2013_0212_58:250159963  1
571     2013_0008_6:250162074   2013_10145_11:250164626  1
572     2013_0008_6:250162074 TMS13F1391P0039:250465621  1
573     2013_0050_8:250169056   2013_10063_19:250164239  1
574     2013_0088_7:250159759    2013_10020_1:250164714  1
575     2013_0108_7:250159843    2013_0154_10:250160394  1
576     2013_0108_7:250159843    2013_0333_17:250162439  1
577     2013_0108_7:250159843     2013_0436_6:250162761  1
578     2013_0109_9:250160030 TMS14F1255P0005:250303597  1
579    2013_0111_12:250160049     2013_0107_8:250159833  1
580    2013_0154_10:250160394    2013_0154_10:250160394  1
581    2013_0154_10:250160394    2013_0436_12:250162767  1
582    2013_0202_46:250160176     2013_0107_6:250159831  1
583    2013_0202_46:250160176     2013_0307_4:250160600  1
584     2013_0212_2:250159907     2013_0109_9:250160030  1
585     2013_0212_2:250159907    2013_0253_11:250160418  1
586    2013_0212_32:250159937     2013_0153_7:250160348  1
587    2013_0212_32:250159937     2013_0154_5:250160358  1
588    2013_0212_32:250159937    2013_10063_7:250164227  1
589    2013_0212_32:250159937    2013_10122_3:250164747  1
590    2013_0212_32:250159937    2013_10309_1:250164479  1
591    2013_0212_55:250159960    2013_0008_20:250162088  1
592    2013_0212_55:250159960     2013_0153_7:250160348  1
593    2013_0212_55:250159960     2013_0333_2:250162423  1
594    2013_0212_58:250159963    2013_0332_42:250161115  1
595     2013_0212_7:250159912   2013_10064_25:250164276  1
596    2013_0216_10:250160702 TMS13F1106P0006:250300932  1
597    2013_0307_10:250160606    2013_0087_14:250159588  1
598    2013_0307_11:250160607    2013_0332_42:250161115  1
599    2013_0307_11:250160607    2013_0333_10:250162431  1
600    2013_0307_12:250160608     2013_0050_8:250169056  1
601    2013_0307_16:250160612    2013_0053_15:250162223  1
602    2013_0307_20:250161028    2013_0111_12:250160049  1
603    2013_0307_20:250161028    2013_0154_10:250160394  1
604    2013_0307_20:250161028    2013_0212_61:250159966  1
605    2013_0307_20:250161028    2013_0333_27:250162449  1
606    2013_0307_20:250161028   2013_10063_19:250164239  1
607    2013_0307_23:250161031    2013_0332_42:250161115  1
608     2013_0307_8:250160604    2013_10084_6:250164723  1
609     2013_0333_2:250162423   2013_10145_23:250164638  1
610    2013_0333_27:250162449    2013_0214_14:250160668  1
611    2013_0333_27:250162449    2013_0214_29:250160683  1
612    2013_0333_27:250162449    2013_0332_42:250161115  1
613    2013_0333_29:250162451     2013_0212_2:250159907  1
614     2013_0333_3:250162424    2013_0212_58:250159963  1
615     2013_0333_3:250162424    2013_0214_14:250160668  1
616     2013_0333_3:250162424    2013_0214_29:250160683  1
617     2013_0333_3:250162424    2013_0216_28:250160720  1
618     2013_0333_3:250162424     2013_0333_3:250162424  1
619     2013_0343_2:250162499     2013_0088_7:250159759  1
620    2013_0343_22:250162550    2013_0053_15:250162223  1
621    2013_0343_22:250162550    2013_0307_16:250160612  1
622    2013_0343_22:250162550          I30572:250253643  1
623    2013_0343_22:250162550    TMS15F1466P0195_A19530  1
624    2013_0343_44:250162573    2013_0307_10:250160606  1
625    2013_0343_44:250162573    2013_10303_2:250164467  1
626     2013_0364_1:250162612     2013_0307_8:250160604  1
627     2013_0364_1:250162612 TMS14F1284P0001:250304001  1
628     2013_0381_5:250162690    2013_10303_2:250164467  1
629    2013_0436_12:250162767    2013_0212_55:250159960  1
630    2013_10020_2:250164715     2013_0324_2:250161035  1
631   2013_10034_19:250164218    2013_0107_10:250159835  1
632   2013_10063_19:250164239     2013_0307_7:250160603  1
633   2013_10063_19:250164239    2013_0333_10:250162431  1
634   2013_10063_19:250164239   2013_10064_25:250164276  1
635   2013_10063_19:250164239    2013_10309_1:250164479  1
636    2013_10084_3:250164720     2013_0107_6:250159831  1
637    2013_10084_6:250164723     2013_0307_6:250160602  1
638    2013_10122_3:250164747     2013_0214_4:250160658  1
639    2013_10122_3:250164747    2013_0307_10:250160606  1
640    2013_10122_3:250164747     2013_0436_4:250162759  1
641    2013_10122_3:250164747    2013_10303_2:250164467  1
642    2013_10122_3:250164747    2013_10309_1:250164479  1
643    2013_10122_5:250164749    2013_0343_22:250162550  1
644    2013_10122_5:250164749   2013_10063_13:250164233  1
645    2013_10303_1:250164466    2013_0212_55:250159960  1
646    2013_10303_1:250164466    2013_0333_10:250162431  1
647    2013_10303_1:250164466    2013_0333_17:250162439  1
648    2013_10303_1:250164466    2013_10124_2:250164352  1
649    2013_10303_1:250164466    2013_10309_1:250164479  1
650    2013_10303_2:250164467     2013_0050_8:250169056  1
651    2013_10303_2:250164467    2013_0087_14:250159588  1
652    2013_10303_2:250164467   2013_10064_25:250164276  1
653    2013_10303_3:250164468    2013_0332_27:250161100  1
654    2013_10303_3:250164468     2013_0339_9:250162492  1
655    2013_10303_3:250164468   2013_10063_19:250164239  1
656    2013_10306_3:250164474    2013_0332_42:250161115  1
657    2013_10306_3:250164474 TMS13F1391P0039:250465621  1
658    2013_10309_1:250164479    2013_0307_11:250160607  1
659    2013_10309_1:250164479     2013_0307_6:250160602  1
660         I000070:250300358    2013_0053_15:250162223  1
661         I000070:250300358     2013_0053_2:250162210  1
662         I000070:250300358 TMS15F1318P0009:250476726  1
663         I000388:250300404         I070126:250164023  1
664         I011335:250300345         I011371:250090769  1
665         I011368:250300318         I011412:250300323  1
666         I011797:250090770    2013_0053_10:250162218  1
667         I030060:250090848   2013_10377_18:250164522  1
668        I030060A:250300227    2013_10020_1:250164714  1
669         I070004:250164022         I070004:250164022  1
670         I070337:250300150     2013_0053_2:250162210  1
671         I070337:250300150     2013_0160_5:250160400  1
672         I070337:250300150    2013_0343_26:250162554  1
673         I090516:250099187     2013_0160_5:250160400  1
674         I090516:250099187 TMS14F1284P0019:250304019  1
675         I090581:250099170         TMEB693:250253991  1
676          I30572:250253643     2013_0160_5:250160400  1
677          I30572:250253643          I30572:250253643  1
678        I9102325:250304510        I9102325:250304510  1
679          I91934:250304625           TMEB1:250253593  1
680          I91934:250304625           TMEB9:250253601  1
681         I930007:250090827    2013_0053_15:250162223  1
682         I930007:250090827    2013_10122_5:250164749  1
683         I930007:250090827 TMS15F1021P0013:250464921  1
684         I930007:250090827 TMS15F1130P0012:250475583  1
685         I930007:250090827 TMS15F1142P0012:250475597  1
686         I940006:250090826         I960557:250300551  1
687         I940239:250300602          I91934:250304625  1
688         I940330:250090830         I011663:250300298  1
689         I940330:250090830         I950379:250300567  1
690         I940561:250090825         I950971:250300591  1
691         I950379:250300567        I8902195:250304523  1
692         I972205:250301855         I070337:250300150  1
693         I972205:250301855         TMEB419:250253865  1
694         I972205:250301855 TMS15F1130P0012:250475583  1
695         I972205:250301855 TMS15F1142P0012:250475597  1
696         I972205:250301855 TMS15F1329P0005:250476750  1
697         I974779:250300473         I980002:250300438  1
698         I992123:250300419         I991702:250090772  1
699         I993073:250300423         I011412:250300323  1
700         M980068:250300452         M980068:250300452  1
701        MM970646:250300486         I930265:250164038  1
702           TMEB1:250253593       I4_2_1425:250304632  1
703         TMEB117:250253666         I011412:250300323  1
704         TMEB117:250253666         I950379:250300567  1
705         TMEB419:250253865   2013_10063_13:250164233  1
706         TMEB419:250253865    2013_10122_5:250164749  1
707         TMEB419:250253865         I940561:250090825  1
708         TMEB693:250253991         I070593:250300163  1
709         TMEB693:250253991         TMEB693:250253991  1
710           TMEB9:250253601          I30572:250253643  1
711 TMS13F1106P0006:250300932    2013_0212_72:250159977  1
712 TMS13F1106P0006:250300932    2013_0214_29:250160683  1
713 TMS13F1106P0006:250300932    2013_0216_15:250160707  1
714 TMS13F1106P0006:250300932    2013_0216_26:250160718  1
715    TMS13F1227P0119_A19491    2013_0053_15:250162223  1
716 TMS14F1035P0004:250302641 TMS14F1310P0004:250301178  1
717 TMS14F1063P0003:250302894 TMS14F1157P0002:250301832  1
718 TMS14F1113P0002:250301450 TMS14F1138P0005:250301674  1
719 TMS14F1113P0002:250301450 TMS14F1157P0002:250301832  1
720 TMS14F1113P0002:250301450 TMS14F1169P0001:250301880  1
721 TMS14F1113P0002:250301450 TMS14F1247P0007:250303518  1
722 TMS14F1138P0005:250301674 TMS14F1171P0004:250301946  1
723 TMS14F1138P0005:250301674 TMS14F1228P0013:250303377  1
724 TMS14F1157P0002:250301832 TMS14F1113P0003:250301451  1
725 TMS14F1157P0002:250301832 TMS14F1244P0006:250303493  1
726 TMS14F1166P0002:250301867 TMS14F1222P0003:250303322  1
727 TMS14F1166P0002:250301867 TMS14F1229P0004:250303381  1
728 TMS14F1166P0002:250301867 TMS14F1247P0003:250303514  1
729 TMS14F1166P0002:250301867 TMS14F1283P0013:250303992  1
730 TMS14F1174P0011:250301981 TMS14F1176P0010:250301997  1
731 TMS14F1174P0011:250301981 TMS14F1247P0003:250303514  1
732 TMS14F1176P0006:250301993 TMS14F1153P0003:250301810  1
733 TMS14F1176P0006:250301993 TMS14F1247P0007:250303518  1
734 TMS14F1176P0010:250301997 TMS14F1174P0011:250301981  1
735 TMS14F1176P0010:250301997 TMS14F1222P0003:250303322  1
736 TMS14F1195P0008:250302099 TMS14F1122P0003:250301540  1
737 TMS14F1240P0004:250303461 TMS14F1213P0007:250302244  1
738 TMS14F1240P0005:250303462 TMS14F1122P0003:250301540  1
739 TMS14F1240P0005:250303462 TMS14F1213P0007:250302244  1
740 TMS14F1240P0005:250303462 TMS14F1228P0013:250303377  1
741 TMS14F1240P0005:250303462 TMS14F1283P0015:250303994  1
742 TMS14F1241P0002:250303465 TMS14F1154P0002:250301819  1
743 TMS14F1247P0007:250303518 TMS14F1107P0004:250301360  1
744 TMS14F1255P0005:250303597     2013_0307_4:250160600  1
745 TMS14F1255P0005:250303597    2013_10303_2:250164467  1
746 TMS14F1255P0005:250303597 TMS14F1288P0001:250304117  1
747 TMS14F1256P0002:250303615 TMS14F1283P0002:250303981  1
748 TMS14F1288P0001:250304117 TMS14F1244P0006:250303493  1
749 TMS14F1300P0002:250300902    TMS15F1463P0054_A19558  1
750 TMS14F1300P0002:250300902    TMS15F1466P0195_A19530  1
751 TMS14F1300P0002:250300902    TMS15F1467P0033_A19532  1
752 TMS14F1310P0004:250301178 TMS14F1035P0004:250302641  1
753 TMS15F1001P0001:250464861 TMS15F1269P0008:250465951  1
754 TMS15F1021P0028:250464932 TMS15F1305P0017:250466080  1
755 TMS15F1021P0028:250464932 TMS15F1318P0009:250476726  1
756 TMS15F1072P0031:250521122 TMS15F1079P0025:250465175  1
757 TMS15F1079P0020:250465173     2013_0307_8:250160604  1
758 TMS15F1109P0003:250465275 TMS15F1100P0005:250465254  1
759 TMS15F1124P0001:250465316 TMS15F1351P0003:250466280  1
760 TMS15F1132P0003:250465370 TMS15F1021P0002:250464910  1
761 TMS15F1132P0013:250475590 TMS15F1196P0010:250465572  1
762 TMS15F1142P0012:250475597 TMS15F1329P0005:250476750  1
763 TMS15F1153P0009:250465409 TMS15F1021P0002:250464910  1
764 TMS15F1153P0009:250465409 TMS15F1073P0005:250465136  1
765 TMS15F1153P0009:250465409 TMS15F1080P0004:250465178  1
766 TMS15F1153P0009:250465409 TMS15F1393P0006:250466543  1
767 TMS15F1154P0002:250518934 TMS15F1351P0003:250466280  1
768 TMS15F1156P0014:250518954 TMS15F1021P0002:250464910  1
769 TMS15F1156P0014:250518954 TMS15F1072P0005:250465127  1
770 TMS15F1156P0014:250518954 TMS15F1079P0020:250465173  1
771 TMS15F1156P0014:250518954 TMS15F1111P0011:250475547  1
772 TMS15F1156P0014:250518954 TMS15F1132P0013:250475590  1
773 TMS15F1159P0001:250518960 TMS15F1318P0022:250476734  1
774 TMS15F1159P0006:250465430         I980505:250090767  1
775 TMS15F1159P0006:250465430 TMS15F1021P0002:250464910  1
776 TMS15F1177P0004:250476294 TMS15F1318P0009:250476726  1
777 TMS15F1196P0010:250465572 TMS15F1153P0009:250465409  1
778 TMS15F1196P0010:250465572 TMS15F1154P0002:250518934  1
779 TMS15F1196P0010:250465572 TMS15F1154P0015:250518942  1
780 TMS15F1196P0010:250465572 TMS15F1156P0014:250518954  1
781 TMS15F1305P0007:250466076 TMS15F1142P0006:250465390  1
782 TMS15F1305P0017:250466080 TMS15F1079P0020:250465173  1
783 TMS15F1305P0017:250466080 TMS15F1159P0006:250465430  1
784 TMS15F1305P0017:250466080 TMS15F1329P0005:250476750  1
785 TMS15F1310P0019:250467021 TMS15F1021P0002:250464910  1
786 TMS15F1310P0019:250467021 TMS15F1196P0010:250465572  1
787 TMS15F1318P0009:250476726 TMS15F1329P0005:250476750  1
788 TMS15F1318P0024:250476735 TMS15F1153P0009:250465409  1
789 TMS15F1318P0024:250476735 TMS15F1156P0014:250518954  1
790 TMS15F1318P0024:250476735 TMS15F1160P0010:250518971  1
791 TMS15F1326P0004:250467063 TMS15F1079P0020:250465173  1
792 TMS15F1326P0004:250467063 TMS15F1195P0010:250465562  1
793 TMS15F1329P0005:250476750         I930007:250090827  1
794 TMS15F1351P0003:250466280 TMS15F1396P0001:250466560  1
795 TMS15F1365P0003:250466326 TMS15F1159P0006:250465430  1
796 TMS15F1367P0001:250475193 TMS15F1021P0003:250464911  1
797 TMS15F1367P0001:250475193 TMS15F1069P0007:250521086  1
798 TMS15F1367P0001:250475193 TMS15F1318P0009:250476726  1
799 TMS15F1396P0001:250466560 TMS15F1351P0003:250466280  1
800 TMS15F1396P0004:250466562 TMS15F1160P0010:250518971  1
801 TMS15F1397P0001:250466568 TMS15F1153P0009:250465409  1
802 TMS15F1398P0008:250466574 TMS15F1130P0007:250465327  1
803 TMS15F1424P0004:250466799 TMS15F1099P0004:250465252  1
804    TMS15F1463P0054_A19558 TMS14F1301P0013:250300938  1
805    TMS18F1024P0005_A19030    TMS18F1047P0024_A18757  1
806    TMS18F1173P0009_A18858    TMS18F1289P0016_A18967  1

correctedped %>% 
  count(SireID,DamID) %$% summary(n)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    3.00    5.55    7.00   77.00

correctedped %>% 
  count(SireID,DamID) %>% 
  filter(n>=5) %>% arrange(desc(n)) %$% union(SireID,DamID) %>% 
  tibble(ParentsMoreThanFiveProg=.) %>%  
  mutate(Cohort=NA,
         Cohort=ifelse(grepl("TMS20",ParentsMoreThanFiveProg,ignore.case = T),"TMS20",
                       ifelse(grepl("TMS19",ParentsMoreThanFiveProg,ignore.case = T),"TMS19",
                              ifelse(grepl("TMS18",ParentsMoreThanFiveProg,ignore.case = T),"TMS18",
                                     ifelse(grepl("TMS17",ParentsMoreThanFiveProg,ignore.case = T),"TMS17",
                                            ifelse(grepl("TMS16",ParentsMoreThanFiveProg,ignore.case = T),"TMS16",
                                                   ifelse(grepl("TMS15",ParentsMoreThanFiveProg,ignore.case = T),"TMS15",
                                                          ifelse(grepl("TMS14",ParentsMoreThanFiveProg,ignore.case = T),"TMS14",
                                                                 ifelse(grepl("TMS13|2013_",ParentsMoreThanFiveProg,
                                                                              ignore.case = T),"TMS13","GGetc"))))))))) %>%
  count(Cohort, name="ParentsWithLeast5offspring")

# A tibble: 4 × 2
  Cohort ParentsWithLeast5offspring
  <chr>                       <int>
1 GGetc                          82
2 TMS13                          77
3 TMS14                          19
4 TMS15                          13

correctedped %>% 
  count(SireID,DamID) %>% 
  arrange(desc(n)) %$% union(SireID,DamID) %>% 
  tibble(Parents=.) %>%  
  mutate(Cohort=NA,
         Cohort=ifelse(grepl("TMS20",Parents,ignore.case = T),"TMS20",
                       ifelse(grepl("TMS19",Parents,ignore.case = T),"TMS19",
                              ifelse(grepl("TMS18",Parents,ignore.case = T),"TMS18",
                                     ifelse(grepl("TMS17",Parents,ignore.case = T),"TMS17",
                                            ifelse(grepl("TMS16",Parents,ignore.case = T),"TMS16",
                                                   ifelse(grepl("TMS15",Parents,ignore.case = T),"TMS15",
                                                          ifelse(grepl("TMS14",Parents,ignore.case = T),"TMS14",
                                                                 ifelse(grepl("TMS13|2013_",Parents,
                                                                              ignore.case = T),"TMS13","GGetc"))))))))) %>%
  count(Cohort, name="Parents")

# A tibble: 5 × 2
  Cohort Parents
  <chr>    <int>
1 GGetc      109
2 TMS13      117
3 TMS14       56
4 TMS15       72
5 TMS18        7

correctedped %>% 
  mutate(Cohort=NA,
         Cohort=ifelse(grepl("TMS20",FullSampleName,ignore.case = T),"TMS20",
                       ifelse(grepl("TMS19",FullSampleName,ignore.case = T),"TMS19",
                              ifelse(grepl("TMS18",FullSampleName,ignore.case = T),"TMS18",
                                     ifelse(grepl("TMS17",FullSampleName,ignore.case = T),"TMS17",
                                            ifelse(grepl("TMS16",FullSampleName,ignore.case = T),"TMS16",
                                                   ifelse(grepl("TMS15",FullSampleName,ignore.case = T),"TMS15",
                                                          ifelse(grepl("TMS14",FullSampleName,ignore.case = T),"TMS14",
                                                                 ifelse(grepl("TMS13|2013_",FullSampleName,
                                                                              ignore.case = T),"TMS13","GGetc"))))))))) %>% 
  count(Cohort, name="BothParentsConfirmed")

  Cohort BothParentsConfirmed
1  GGetc                   20
2  TMS13                 1786
3  TMS14                 1303
4  TMS15                  589
5  TMS17                   11
6  TMS18                  592
7  TMS19                   40
8  TMS20                  132

–> Write verified pedigree

correctedped %>% 
  write.table(.,here::here("output","verified_ped.txt"),
              row.names = F, col.names = T, quote = F)

Next Step

Preprocess data files: Prepare haplotype and dosage matrices, GRMs, pedigree and BLUPs, genetic map and recombination frequency matrix, for use in predictions.

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] magrittr_2.0.1  forcats_0.5.1   stringr_1.4.0   dplyr_1.0.7    
 [5] purrr_0.3.4     readr_2.0.1     tidyr_1.1.3     tibble_3.1.3   
 [9] ggplot2_3.3.5   tidyverse_1.3.1 workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7        here_1.0.1        lubridate_1.7.10  assertthat_0.2.1 
 [5] rprojroot_2.0.2   digest_0.6.27     utf8_1.2.2        R6_2.5.0         
 [9] cellranger_1.1.0  backports_1.2.1   reprex_2.0.1      evaluate_0.14    
[13] highr_0.9         httr_1.4.2        pillar_1.6.2      rlang_0.4.11     
[17] readxl_1.3.1      rstudioapi_0.13   whisker_0.4       jquerylib_0.1.4  
[21] rmarkdown_2.10    labeling_0.4.2    bit_4.0.4         munsell_0.5.0    
[25] broom_0.7.9       compiler_4.1.0    httpuv_1.6.1      modelr_0.1.8     
[29] xfun_0.25         pkgconfig_2.0.3   htmltools_0.5.1.1 tidyselect_1.1.1 
[33] fansi_0.5.0       crayon_1.4.1      tzdb_0.1.2        dbplyr_2.1.1     
[37] withr_2.4.2       later_1.2.0       grid_4.1.0        jsonlite_1.7.2   
[41] gtable_0.3.0      lifecycle_1.0.0   DBI_1.1.1         git2r_0.28.0     
[45] scales_1.1.1      cli_3.0.1         stringi_1.7.3     vroom_1.5.4      
[49] farver_2.1.0      fs_1.5.0          promises_1.2.0.1  xml2_1.3.2       
[53] bslib_0.2.5.1     ellipsis_0.3.2    generics_0.1.0    vctrs_0.3.8      
[57] tools_4.1.0       bit64_4.0.5       glue_1.4.2        hms_1.1.0        
[61] parallel_4.1.0    yaml_2.2.1        colorspace_2.0-2  rvest_1.0.1      
[65] knitr_1.33        haven_2.4.3       sass_0.4.0

Verify the pedigree entries

Marnin Wolfe

2021-May-12