Last updated: 2021-05-05
Checks: 7 0
Knit directory: NRCRI_2021GS/
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Untracked: output/genomicPredictions_NRCRI_2021May03.csv
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Modified: README.md
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/convertDCas21_5841_ToVCF.Rmd) and HTML (docs/convertDCas21_5841_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 |
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| html | e8b3eeb | wolfemd | 2021-05-03 | Build site. |
| Rmd | c887639 | wolfemd | 2021-05-03 | Publish site up through cleanTPdata step to generate cleaned TP data before continuing pipeline. |
cd /home/jj332_cas/marnin/NRCRI_2021GS;
# Initiate "screen" and then R#' @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)
dartvcfInput<-here::here("data/Report-DCas21-5841","Report_5841_VCF_Ref_Version6.txt")
dartcountsInput<-here::here("data/Report-DCas21-5841","Report_5841_Counts_Ref_Version6.csv")
outName<-here::here("data/Report-DCas21-5841","DCas21_5841")
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 443
dim(readCounts)
# [1] 27206 477
#
#
# # Initial look at names....
colnames(readCounts)[1:100]
# [1] "AlleleID"
# [2] "CloneID"
# [3] "ClusterTempIndex"
# [4] "AlleleSequence"
# [5] "TrimmedSequence"
# [6] "TrimmedSequence_plus_Strand"
# [7] "Short"
# [8] "Lowcomplexity"
# [9] "Chrom_Cassava_v61"
# [10] "ChromPos_Cassava_v61"
# [11] "SNP_ChromPos_Cassava_v61"
# [12] "AlnCnt_Cassava_v61"
# [13] "AlnEvalue_Cassava_v61"
# [14] "Strand_Cassava_v61"
# [15] "SeqDiff_Cassava_v61"
# [16] "ClusterConsensusSequence"
# [17] "ClusterSize"
# [18] "AlleleSeqDist"
# [19] "SNP"
# [20] "SnpPosition"
# [21] "CallRate"
# [22] "OneRatioRef"
# [23] "OneRatioSnp"
# [24] "FreqHomRef"
# [25] "FreqHomSnp"
# [26] "FreqHets"
# [27] "PICRef"
# [28] "PICSnp"
# [29] "AvgPIC"
# [30] "AvgCountRef"
# [31] "AvgCountSnp"
# [32] "RatioAvgCountRefAvgCountSnp"
# [33] "FreqHetsMinusFreqMinHom"
# [34] "AlleleCountsCorrelation"
# [35] "aggregateTagsTotal"
# [36] "DerivedCorrMinusSeedCorr"
# [37] "RepRef"
# [38] "RepSNP"
# [39] "RepAvg"
# [40] "PicRepRef"
# [41] "PicRepSNP"
# [42] "TotalPicRepRefTest"
# [43] "TotalPicRepSnpTest"
# [44] "NR20.NG.C3.Cass.0001_C01...NR20C3F1P0003"
# [45] "NR20.NG.C3.Cass.0001_D01...NR20C3F1P0004"
# [46] "NR20.NG.C3.Cass.0001_E01...NR20C3F1P0005"
# [47] "NR20.NG.C3.Cass.0001_F01...NR20C3F1P0006"
# [48] "NR20.NG.C3.Cass.0001_G01...NR20C3F1P0007"
# [49] "NR20.NG.C3.Cass.0001_H01...NR20C3F2P0001"
# [50] "NR20.NG.C3.Cass.0001_A02...NR20C3F2P0003"
# [51] "NR20.NG.C3.Cass.0001_B02...NR20C3F2P0004"
# [52] "NR20.NG.C3.Cass.0001_C02...NR20C3F2P0005"
# [53] "NR20.NG.C3.Cass.0001_D02...NR20C3F2P0006"
# [54] "NR20.NG.C3.Cass.0001_E02...NR20C3F2P0007"
# [55] "NR20.NG.C3.Cass.0001_F02...NR20C3F2P0008"
# [56] "NR20.NG.C3.Cass.0001_H02...NR20C3F2P0010"
# [57] "NR20.NG.C3.Cass.0001_A03...NR20C3F2P0011"
# [58] "NR20.NG.C3.Cass.0001_B03...NR20C3F2P0012"
# [59] "NR20.NG.C3.Cass.0001_C03...NR20C3F2P0013"
# [60] "NR20.NG.C3.Cass.0001_D03...NR20C3F2P0014"
colnames(vcf)[1:30]
# [1] "X.CHROM"
# [2] "POS"
# [3] "ID"
# [4] "REF"
# [5] "ALT"
# [6] "QUAL"
# [7] "FILTER"
# [8] "INFO"
# [9] "FORMAT"
# [10] "NR20.NG.C3.Cass.0001_A01...NR20C3F1P0001"
# [11] "NR20.NG.C3.Cass.0001_A10...NR20C3F4P0007"
# [12] "NR20.NG.C3.Cass.0001_A11...NR20C3F4P0016"
# [13] "NR20.NG.C3.Cass.0001_A12...NR20C3F4P0025"
# [14] "NR20.NG.C3.Cass.0001_A02...NR20C3F2P0003"
# [15] "NR20.NG.C3.Cass.0001_A03...NR20C3F2P0011"
# [16] "NR20.NG.C3.Cass.0001_A04...NR20C3F2P0020"
# [17] "NR20.NG.C3.Cass.0001_A05...NR20C3F2P0028"
# [18] "NR20.NG.C3.Cass.0001_A06...NR20C3F3P0003"
# [19] "NR20.NG.C3.Cass.0001_A07...NR20C3F3P0011"
# [20] "NR20.NG.C3.Cass.0001_A08...NR20C3F3P0021"
# [21] "NR20.NG.C3.Cass.0001_A09...NR20C3F3P0030"
# [22] "NR20.NG.C3.Cass.0001_B01...NR20C3F1P0002"
# [23] "NR20.NG.C3.Cass.0001_B10...NR20C3F4P0008"
# [24] "NR20.NG.C3.Cass.0001_B11...NR20C3F4P0017"
# [25] "NR20.NG.C3.Cass.0001_B12...NR20C3F4P0026"
# [26] "NR20.NG.C3.Cass.0001_B02...NR20C3F2P0004"
# [27] "NR20.NG.C3.Cass.0001_B03...NR20C3F2P0012"
# [28] "NR20.NG.C3.Cass.0001_B04...NR20C3F2P0021"
# [29] "NR20.NG.C3.Cass.0001_B05...NR20C3F2P0029"
# [30] "NR20.NG.C3.Cass.0001_B06...NR20C3F3P0004"
# rm(vcf,readCounts); gc()Available and sourced from code/ subdirectory: convertDart2vcf.R.
source(here::here("code/","convertDart2vcf.R"))
convertDart2vcf(dartvcfInput,dartcountsInput,outName,
nskipvcf=2,nskipcounts=3,ncores)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-DCas21-5841","DCas21_5841.vcf.gz")
filters<-"--minDP 4 --maxDP 50" # because using GT not PL for impute (Beagle5)
outPath<-here::here("data/Report-DCas21-5841/")
outSuffix<-"DCas21_5841"
future_map(1:18,
~splitVCFbyChr(Chr=.,
vcfIn=vcfIn,filters=filters,
outPath=outPath,outSuffix=outSuffix))
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/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_1.0.6 whisker_0.4 knitr_1.32 magrittr_2.0.1
[5] R6_2.5.0 rlang_0.4.10 fansi_0.4.2 stringr_1.4.0
[9] tools_4.0.3 xfun_0.22 utf8_1.2.1 git2r_0.28.0
[13] jquerylib_0.1.3 htmltools_0.5.1.1 ellipsis_0.3.1 rprojroot_2.0.2
[17] yaml_2.2.1 digest_0.6.27 tibble_3.1.1 lifecycle_1.0.0
[21] crayon_1.4.1 later_1.1.0.1 sass_0.3.1 vctrs_0.3.7
[25] promises_1.2.0.1 fs_1.5.0 glue_1.4.2 evaluate_0.14
[29] rmarkdown_2.7 stringi_1.5.3 bslib_0.2.4 compiler_4.0.3
[33] pillar_1.6.0 jsonlite_1.7.2 httpuv_1.5.5 pkgconfig_2.0.3