Last updated: 2021-01-21

Checks: 7 0

Knit directory: TARI_2020GS/

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Unstaged changes:
    Modified:   analysis/01-cleanTPdata.Rmd
    Modified:   analysis/02-GetBLUPs.Rmd
    Modified:   analysis/03-CrossValidation.Rmd
    Modified:   analysis/04-GetGBLUPs.Rmd
    Modified:   analysis/05-Results.Rmd
    Modified:   analysis/index.Rmd
    Modified:   output/TARI_trials_NOT_identifiable.csv
    Modified:   output/maxNOHAV_byStudy.csv

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/convertDCas20_5629_ToVCF.Rmd) and HTML (docs/convertDCas20_5629_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 abaf52a wolfemd 2020-12-23 Build site.
Rmd fae176a wolfemd 2020-12-23 Publish the first set of analyses and files for TARI 2020 GS.

cd /home/jj332_cas/marnin/TARI_2020GS

Input Parameters

#' @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-DCas20-5629","Report_5629_VCF_Ref_Version6.txt")
dartcountsInput<-here::here("data/Report-DCas20-5629","Report_5629_Counts_Ref_Version6.csv")
outName<-here::here("data/Report-DCas20-5629","DCas20_5629")
nskipvcf<-2 
nskipcounts<-3
ncores<-10

Prelim. check format

Start 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  3157
dim(readCounts)
# [1] 27206  3191
# 
# 
# # 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"          "C1GS_A01...TZMRK180001"     
 # [45] "C1GS_B01...TZMRK180001"      "C1GS_C01...TZMRK180001"     
 # [47] "C1GS_D01...TZMRK180001"      "C1GS_E01...TZMRK180001"     
 # [49] "C1GS_F01...TZMRK180001"      "C1GS_G01...TZMRK180001"     
 # [51] "C1GS_H01...TZMRK180001"      "C1GS_A02...TZMRK180001"     
 # [53] "C1GS_B02...TZMRK180001"      "C1GS_C02...TZMRK180001"     
 # [55] "C1GS_D02...TZMRK180001"      "C1GS_E02...TZMRK180001"     
 # [57] "C1GS_F02...TZMRK180001"      "C1GS_G02...TZMRK180001" 
colnames(vcf)[1:30]
#  [1] "X.CHROM"                "POS"                    "ID"                    
#  [4] "REF"                    "ALT"                    "QUAL"                  
#  [7] "FILTER"                 "INFO"                   "FORMAT"                
# [10] "C1GS_A01...TZMRK180001" "C1GS_A10...TZMRK180001" "C1GS_A11...TZMRK180001"
# [13] "C1GS_A02...TZMRK180001" "C1GS_A03...TZMRK180001" "C1GS_A04...TZMRK180001"
# [16] "C1GS_A05...TZMRK180001" "C1GS_A06...TZMRK180001" "C1GS_A07...TZMRK180001"
# [19] "C1GS_A08...TZMRK180001" "C1GS_A09...TZMRK180001" "C1GS_B01...TZMRK180001"
# [22] "C1GS_B10...TZMRK180001" "C1GS_B11...TZMRK180001" "C1GS_B12...TZMRK180001"
# [25] "C1GS_B02...TZMRK180001" "C1GS_B03...TZMRK180001" "C1GS_B04...TZMRK180001"
# [28] "C1GS_B05...TZMRK180001" "C1GS_B06...TZMRK180001" "C1GS_B07...TZMRK180001"

# rm(vcf,readCounts); gc()

Conversion function

Available and sourced from code/ subdirectory: convertDart2vcf.R.

Run conversion function

source(here::here("code/","convertDart2vcf.R"))
convertDart2vcf(dartvcfInput,dartcountsInput,outName,
                nskipvcf=2,nskipcounts=3,ncores)

Genomewide to per-chrom VCFs

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-DCas20-5629","DCas20_5629.vcf.gz")
filters<-"--minDP 4 --maxDP 50" # because using GT not PL for impute (Beagle5)
outPath<-here::here("data/Report-DCas20-5629")
outSuffix<-"DCas20_5629"

future_map(1:18,
           ~splitVCFbyChr(Chr=.,
                          vcfIn=vcfIn,filters=filters,
                          outPath=outPath,outSuffix=outSuffix))

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

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      rstudioapi_0.13 whisker_0.4     knitr_1.30     
 [5] magrittr_2.0.1  R6_2.5.0        rlang_0.4.10    stringr_1.4.0  
 [9] tools_4.0.2     xfun_0.20       git2r_0.28.0    htmltools_0.5.1
[13] ellipsis_0.3.1  rprojroot_2.0.2 yaml_2.2.1      digest_0.6.27  
[17] tibble_3.0.5    lifecycle_0.2.0 crayon_1.3.4    later_1.1.0.1  
[21] vctrs_0.3.6     promises_1.1.1  fs_1.5.0        glue_1.4.2     
[25] evaluate_0.14   rmarkdown_2.6   stringi_1.5.3   compiler_4.0.2 
[29] pillar_1.4.7    httpuv_1.5.5    pkgconfig_2.0.3