Last updated: 2021-08-26
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screen;
cd ~/IITA_2021GS/;
R;devtools::install_github("wolfemd/genomicMateSelectR", ref = 'master') library(tidyverse); library(magrittr);
library(genomicMateSelectR)
dartvcfInput<-here::here("data/Report-DCas21-6038","Report_6038_VCF_Ref_Version6.txt")
dartcountsInput<-here::here("data/Report-DCas21-6038","Report_6038_Counts_Ref_Version6.csv")
outName<-here::here("data/Report-DCas21-6038","DCas21_6038")
nskipvcf<-2; nskipcounts<-3; ncores<-20Manual check that the files read in corretly.
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 1485
dim(readCounts)
# [1] 27206 1519
#
# # Initial look at names....
colnames(readCounts)[1:100]
# [1] "AlleleID" "CloneID"
# [3] "ClusterTempIndex" "AlleleSequence"
# [5] "TrimmedSequence" "TrimmedSequence_plus_Strand"
# [7] "Short" "Lowcomplexity"
# [9] "Chrom_Cassava_v61" "ChromPos_Cassava_v61"
# [11] "SNP_ChromPos_Cassava_v61" "AlnCnt_Cassava_v61"
# [13] "AlnEvalue_Cassava_v61" "Strand_Cassava_v61"
# [15] "SeqDiff_Cassava_v61" "ClusterConsensusSequence"
# [17] "ClusterSize" "AlleleSeqDist"
# [19] "SNP" "SnpPosition"
# [21] "CallRate" "OneRatioRef"
# [23] "OneRatioSnp" "FreqHomRef"
# [25] "FreqHomSnp" "FreqHets"
# [27] "PICRef" "PICSnp"
# [29] "AvgPIC" "AvgCountRef"
# [31] "AvgCountSnp" "RatioAvgCountRefAvgCountSnp"
# [33] "FreqHetsMinusFreqMinHom" "AlleleCountsCorrelation"
# [35] "aggregateTagsTotal" "DerivedCorrMinusSeedCorr"
# [37] "RepRef" "RepSNP"
# [39] "RepAvg" "PicRepRef"
# [41] "PicRepSNP" "TotalPicRepRefTest"
# [43] "TotalPicRepSnpTest" "TMS20F1286P0032_A35051"
# [45] "IITA.TMS.IBA090454_A35123" "TMS20F1583P0053_A35131"
# [47] "TMS20F1048P0026_A35138" "TMS20F1286P0007_A35059"
# [49] "TMS20F1677P0003_A35067" "TMS20F1679P0035_A35075"
# [51] "TMS20F1613P0027_A35083" "TMS20F1286P0017_A35091"
# [53] "IITA.TMS.IBA090091_A35099" "TMS20F1621P0005_A35107"
# [55] "TMS20F1621P0001_A35115" "TMS20F1613P0022_A35052"
# [57] "TMS20F1679P0037_A35124" "TMS20F1589P0087_A35132"
# [59] "TMS20F1048P0031_A35139" "TMS20F1582P0024_A35060"
# [61] "TMS20F1589P0070_A35068" "IITA.TMS.IBA051632_A35076"
# [63] "TMS20F1613P0032_A35084" "TMS20F1590P0055_A35092"
colnames(vcf)[1:30]
# [1] "X.CHROM" "POS"
# [3] "ID" "REF"
# [5] "ALT" "QUAL"
# [7] "FILTER" "INFO"
# [9] "FORMAT" "TMS20F1286P0032_A35051"
# [11] "IITA.TMS.IBA090454_A35123" "TMS20F1583P0053_A35131"
# [13] "TMS20F1048P0026_A35138" "TMS20F1286P0007_A35059"
# [15] "TMS20F1677P0003_A35067" "TMS20F1679P0035_A35075"
# [17] "TMS20F1613P0027_A35083" "TMS20F1286P0017_A35091"
# [19] "IITA.TMS.IBA090091_A35099" "TMS20F1621P0005_A35107"
# [21] "TMS20F1621P0001_A35115" "TMS20F1613P0022_A35052"
# [23] "TMS20F1679P0037_A35124" "TMS20F1589P0087_A35132"
# [25] "TMS20F1048P0031_A35139" "TMS20F1582P0024_A35060"
# [27] "TMS20F1589P0070_A35068" "IITA.TMS.IBA051632_A35076"
# [29] "TMS20F1613P0032_A35084" "TMS20F1590P0055_A35092"
# rm(vcf,readCounts); gc()genomicMateSelectR::convertDart2vcf(dartvcfInput,dartcountsInput,outName,
nskipvcf=2,nskipcounts=3,ncores)
# VCF written successfully
# However, see warnings for future function dev.
# 5: The `path` argument of `write_lines()` is deprecated as of readr 1.4.0.
# Please use the `file` argument instead.
# This warning is displayed once every 8 hours.
# Call `lifecycle::last_warnings()` to see where this warning was generated.
# 6: In write.table(tmp, paste0(outName, ".vcf"), append = T, sep = "\t", :
# appending column names to fileSplit the genome-wide VCF into per-chromosome VCFs for imputation.
require(furrr); plan(multisession, workers = 18)
options(future.globals.maxSize=+Inf); options(future.rng.onMisuse="ignore")
vcfIn<-here::here("data/Report-DCas21-6038","DCas21_6038.vcf.gz")
filters<-"--minDP 4 --maxDP 50" # because using GT not PL for impute (Beagle5)
outPath<-here::here("data/Report-DCas21-6038/")
outSuffix<-"DCas21_6038"
future_map(1:18,
~genomicMateSelectR::splitVCFbyChr(Chr=.,
vcfIn=vcfIn,filters=filters,
outPath=outPath,
outSuffix=outSuffix))
plan(sequential)
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] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 whisker_0.4 knitr_1.33 magrittr_2.0.1
[5] R6_2.5.0 rlang_0.4.11 fansi_0.5.0 stringr_1.4.0
[9] tools_4.1.0 xfun_0.25 utf8_1.2.2 git2r_0.28.0
[13] jquerylib_0.1.4 htmltools_0.5.1.1 ellipsis_0.3.2 rprojroot_2.0.2
[17] yaml_2.2.1 digest_0.6.27 tibble_3.1.3 lifecycle_1.0.0
[21] crayon_1.4.1 later_1.2.0 sass_0.4.0 vctrs_0.3.8
[25] promises_1.2.0.1 fs_1.5.0 glue_1.4.2 evaluate_0.14
[29] rmarkdown_2.10 stringi_1.7.3 bslib_0.2.5.1 compiler_4.1.0
[33] pillar_1.6.2 jsonlite_1.7.2 httpuv_1.6.1 pkgconfig_2.0.3