Last updated: 2020-10-09
Checks: 7 0
Knit directory: NaCRRI_2020GS/
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Unstaged changes:
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Deleted: analysis/Imputation_EMBRAPA_102419.Rmd
Deleted: analysis/ImputeDCas20_5360.Rmd
Deleted: analysis/Verify_gbs2dart_sampleMatches_EMBRAPA_102419.Rmd
Deleted: analysis/convertDCas19_4403_ToVCF_102419.Rmd
Deleted: analysis/convertDCas20_5360_ToVCF.Rmd
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/convertDCas20_5419_ToVCF.Rmd) and HTML (docs/convertDCas20_5419_ToVCF.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 | c6022b6 | wolfemd | 2020-10-09 | Build site. |
| Rmd | 4f8a229 | wolfemd | 2020-10-09 | Publish imputations for 2020 of DCAs20_5360 (and 2019 code too) for |
#' @dartvcfInput input name and path of "vcf" file from DArT
#' @dartcountsInput input name and path of counts file from DArT
#' @outName output path and name
#' @nskipvcf number of "VCF" rows to skip on read-in
#' @nskipcounts number of "counts file" rows to skip on read in
#' @ncores number of cores to use, could be VERY memory intensive
#' @dartVars chr vector, column names that _are not_ sample IDs in the read-counts file. I use this internally to assign the sampleIDs in the VCF file
library(tidyverse); library(magrittr)
dartvcfInput<-here::here("data/Report-DCas20-5419","Report_5419_VCF_Ref_Version6.txt")
dartcountsInput<-here::here("data/Report-DCas20-5419","Report_5419_Counts_Ref_Version6.csv")
outName<-here::here("data/Report-DCas20-5419","DCas20_5419")
nskipvcf<-2
nskipcounts<-3
ncores<-10Start manual. Check that the files read in according to previous code. Adjust code if necessary. Make a function and apply it to the input files.
# vcf<-read.table(dartvcfInput,
# stringsAsFactors = F,skip = nskipvcf, header = T, sep = "\t", comment.char = "")
# readCounts<-read.csv(dartcountsInput, stringsAsFactors = F,header = T,skip=nskipcounts)
#
# dim(vcf)
# # [1] 13603 2052
# dim(readCounts)
# # [1] 27206 2068
#
# # the lenghts don't match?
#
# # Initial look at names....
# colnames(readCounts)[1:100]
# # [1] "AlleleID" "CloneID"
# # [3] "AlleleSequence" "TrimmedSequence"
# # [5] "TrimmedSequence_plus_Strand" "Chrom_Cassava_v61"
# # [7] "Tag_ChromPos_Cassava_v61" "SNP_ChromPos_Cassava_v61"
# # [9] "AlnCnt_Cassava_v61" "AlnEvalue_Cassava_v61"
# # [11] "Strand_Cassava_v61" "SNP"
# # [13] "SnpPosition" "CallRate"
# # [15] "OneRatioRef" "OneRatioSnp"
# # [17] "FreqHomRef" "FreqHomSnp"
# # [19] "FreqHets" "PICRef"
# # [21] "PICSnp" "AvgPIC"
# # [23] "AvgCountRef" "AvgCountSnp"
# # [25] "RepAvg" "GS_Prediction_NaCRRI_2019_2"
# # [27] "GS_Prediction_NaCRRI_2019_1" "GS_Prediction_NaCRRI_2019_26"
# # [29] "GS_Prediction_NaCRRI_2019_28" "GS_Prediction_NaCRRI_2019_64"
# # [31] "GS_Prediction_NaCRRI_2019_77" "GS_Prediction_NaCRRI_2019_92"
# # [33] "GS_Prediction_NaCRRI_2019_80" "GS_Prediction_NaCRRI_2019_3"
# # [35] "GS_Prediction_NaCRRI_2019_14" "GS_Prediction_NaCRRI_2019_52"
# colnames(vcf)[1:30]
# # [1] "X.CHROM" "POS"
# # [3] "ID" "REF"
# # [5] "ALT" "QUAL"
# # [7] "FILTER" "INFO"
# # [9] "FORMAT" "GS_Prediction_NaCRRI_2019_2"
# # [11] "GS_Prediction_NaCRRI_2019_11" "GS_Prediction_NaCRRI_2019_12"
# # [13] "GS_Prediction_NaCRRI_2019_13" "GS_Prediction_NaCRRI_2019_3"
# # [15] "GS_Prediction_NaCRRI_2019_4" "GS_Prediction_NaCRRI_2019_5"
# # [17] "GS_Prediction_NaCRRI_2019_6" "GS_Prediction_NaCRRI_2019_7"
# # [19] "GS_Prediction_NaCRRI_2019_8" "GS_Prediction_NaCRRI_2019_9"
# # [21] "GS_Prediction_NaCRRI_2019_10" "GS_Prediction_NaCRRI_2019_1"
# # [23] "GS_Prediction_NaCRRI_2019_23" "GS_Prediction_NaCRRI_2019_24"
# # [25] "GS_Prediction_NaCRRI_2019_25" "GS_Prediction_NaCRRI_2019_14"
# # [27] "GS_Prediction_NaCRRI_2019_15" "GS_Prediction_NaCRRI_2019_17"
# # [29] "GS_Prediction_NaCRRI_2019_18" "GS_Prediction_NaCRRI_2019_19"
# Need to add a check in the conversion function
# that matches the names and reorders if necessary...
#... turns out, the function already checks for that!!
# But seriously... the two outputs should come in the same order to avoid downstream problems.Available and sourced from code/ subdirectory: convertDart2vcf.R.
Split the genome-wide VCF into per-chromosome VCFs for imputation.
require(furrr); options(mc.cores=18); plan(multiprocess)
source(here::here("code","imputationFunctions.R"))
vcfIn<-here::here("data/Report-DCas20-5419","DCas20_5419.vcf.gz")
filters<-"--minDP 4 --maxDP 50" # because using GT not PL for impute (Beagle5)
outPath<-here::here("data/Report-DCas20-5419/")
outSuffix<-"DCas20_5419"
future_map(1:18,
~splitVCFbyChr(Chr=.,
vcfIn=vcfIn,filters=filters,
outPath=outPath,outSuffix=outSuffix))2043 clones, 12981 SNP
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 whisker_0.4 knitr_1.30 magrittr_1.5
[5] R6_2.4.1 rlang_0.4.7 stringr_1.4.0 tools_4.0.2
[9] xfun_0.18 git2r_0.27.1 htmltools_0.5.0 ellipsis_0.3.1
[13] yaml_2.2.1 digest_0.6.25 rprojroot_1.3-2 tibble_3.0.3
[17] lifecycle_0.2.0 crayon_1.3.4 later_1.1.0.1 vctrs_0.3.4
[21] promises_1.1.1 fs_1.5.0 glue_1.4.2 evaluate_0.14
[25] rmarkdown_2.4 stringi_1.5.3 compiler_4.0.2 pillar_1.4.6
[29] backports_1.1.10 httpuv_1.5.4 pkgconfig_2.0.3