Last updated: 2020-09-01

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Knit directory: EMBRAPA_2020GS/

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File	Version	Author	Date	Message
Rmd	6e27397	wolfemd	2020-09-01	EMBRAPA C2 has been imputed. Publish report and share to cassavabase
html	ed70a5a	wolfemd	2020-08-26	Build site.
Rmd	bcd83b4	wolfemd	2020-08-26	Initial publish (prior to running imputation). Debugging will be
Rmd	9d4dfab	wolfemd	2020-08-26	Code organized into functions. Ready to run imputation of C2?

DArTseqLD (DCas20-5360) arrived on Aug. 22, 2020. Contains GS C2 for EMBRAPA.

Last year’s reference panel for imputation had ~64K SNP. The C1 progeny imputed by it had <9K SNP after post-imputation filters.

Options to proceed with imputation of C2 (DCas20-5360):

Last year’s reference panel, without C1 (64K SNP)
Last year’s reference panel + C1 (reduce refpanel to sites passing post-impute filter in C1 = 9K SNP)
Last year’s ref. panel + C1 (include unfiltered C1 data = 64K refpanel SNP)

If I can use Beagle5 or latest, should be possible (fast) to create all 3 and compare the results using PCA, prediction, correlation of kinship matrices, etc.

Impute EMBRAPA GS C2

Copy the imputation reference panel from 2019 to the data/ folder.

cp /home/jj332_cas/marnin/EMBRAPA_2020GS /workdir/mw489/
cp /home/jj332_cas/CassavaGenotypeData/nextgenImputation2019/ImputationEMBRAPA_102419/chr*_ImputationReferencePanel_EMBRAPA_Phased_102619.vcf.gz /workdir/mw489/EMBRAPA_2020GS/data/
cp -r /home/jj332_cas/marnin/EMBRAPA_2020GS/code /workdir/mw489/EMBRAPA_2020GS/
cp -r /home/jj332_cas/CassavaGenotypeData/CassavaGeneticMap /workdir/mw489/EMBRAPA_2020GS/data/
cp /home/jj332_cas/CassavaGenotypeData/nextgenImputation2019/ImputationEMBRAPA_102419/chr*_EMBRAPA_C1progeny_FromDCas19_4301_*  /workdir/mw489/EMBRAPA_2020GS/data/

RefPanel: Exclude C1

Impute with Beagle V5.0.

Use the “imputation reference panel” dataset from 2019, e.g. chr1_ImputationReferencePanel_EMBRAPA_Phased_102619.vcf.gz as reference.

Requires 1 large memory Cornell CBSU machine (e.g. cbsulm17; 112 cores, 512 GB RAM), running 1 chromosome at a time.

R functions are stored in the code/ sub-directory. Functions sourced from e.g. imputationFunctions.R are wrappers around e.g. Beagle, and other command line programs.

targetVCFpath<-here::here("data/Report-DCas20-5360/") # location of the targetVCF
refVCFpath<-here::here("data/")
mapPath<-here::here("data/CassavaGeneticMap/")
outPath<-here::here("output/")
samplesToExclude<-here::here("data","samplesToExclude.txt")
outSuffix<-"DCas20_5360"

Found a sample “A.Preto.joselito” in target VCF that is already in the refpanel, so I must exclude it. Created a file data/samplesToExclude.txt to give to Beagle.

bcftools query \
  --list-samples /home/jj332_cas/CassavaGenotypeData/nextgenImputation2019/ImputationEMBRAPA_102419/chr1_ImputationReferencePanel_EMBRAPA_Phased_102619.vcf.gz > /home/jj332_cas/marnin/EMBRAPA_2020GS/data/chr1_ImputationReferencePanel_EMBRAPA_Phased_102619.samples

refpanel_samples<-read.table(here::here("data","chr1_ImputationReferencePanel_EMBRAPA_Phased_102619.samples"), 
                             header=F, stringsAsFactors = F)$V1
target_samples<-read.table(here::here("data/Report-DCas20-5360/","DCas20_5360.samples"), 
                             header=F, stringsAsFactors = F)$V1
samplesToExclude<-target_samples[target_samples %in% refpanel_samples]
length(samplesToExclude) # [1] 644
write.table(samplesToExclude,file=here::here("data","samplesToExclude.txt"),row.names = F, col.names = F, quote = F)

Impute C2

source(here::here("code","imputationFunctions.R"))

purrr::map(1:18,~runBeagle5(targetVCF=paste0(targetVCFpath,"chr",.,"_DCas20_5360.vcf.gz"),
                            refVCF=paste0(refVCFpath,"chr",.,"_ImputationReferencePanel_EMBRAPA_Phased_102619.vcf.gz"),
                            mapFile=paste0(mapPath,"chr",.,"_cassava_cM_pred.v6_91019.map"),
                            outName=paste0(outPath,"chr",.,"_DCas20_5360_REFimputed"),
                            samplesToExclude=samplesToExclude,
                            nthreads=112))

Clean up Beagle log files after run. Move to sub-directory output/BeagleLogs/.

cd /workdir/mw489/EMBRAPA_2020GS/output/; 
mkdir BeagleLogs;
cp *_DCas20_5360_REFimputed.log BeagleLogs/
cp -r BeagleLogs /home/jj332_cas/marnin/EMBRAPA_2020GS/output/
cp *_DCas20_5360_REFimputed* /home/jj332_cas/marnin/EMBRAPA_2020GS/output/

Post-impute filter

For now, the function will just do a fixed filter: AR2>0.75 (DR2>0.75 as of Beagle5.0), P_HWE>1e-20, MAF>0.005 [0.5%].

It can easily be modified in the future to include parameters to vary the filter specifications.

Input parameters

#' @inPath path to input VCF-to-be-filtered, can be left null if path included in @inName . Must end in "/"
#' @inName name of input VCF file EXCLUDING file extension. Assumes .vcf.gz
#' @outPath path where filtered VCF and related are to be stored.Can be left null if path included in @outName . Must end in "/".
#' @outName name desired for output EXCLUDING extension. Output will be .vcf.gz

Loop to filter all 18 VCF files in parallel

inPath<-here::here("output/")
outPath<-here::here("output/")
source(here::here("code","imputationFunctions.R"))
require(furrr); options(mc.cores=ncores); plan(multiprocess)
future_map(1:18,~postImputeFilter(inPath=inPath,
                                  inName=paste0("chr",.,"_DCas20_5360_REFimputed"),
                                  outPath=outPath,
                                  outName=paste0("chr",.,"_DCas20_5360_REFimputedAndFiltered")))
# [1] "1068 sites passing filter"
# [1] "Filtering Complete: chr1_DCas20_5360_REFimputedAndFiltered"
# [1] "437 sites passing filter"
# [1] "Filtering Complete: chr2_DCas20_5360_REFimputedAndFiltered"
# [1] "559 sites passing filter"
# [1] "Filtering Complete: chr3_DCas20_5360_REFimputedAndFiltered"
# [1] "207 sites passing filter"
# [1] "Filtering Complete: chr4_DCas20_5360_REFimputedAndFiltered"
# [1] "783 sites passing filter"
# [1] "Filtering Complete: chr5_DCas20_5360_REFimputedAndFiltered"
# [1] "447 sites passing filter"
# [1] "Filtering Complete: chr6_DCas20_5360_REFimputedAndFiltered"
# [1] "238 sites passing filter"
# [1] "Filtering Complete: chr7_DCas20_5360_REFimputedAndFiltered"
# [1] "409 sites passing filter"
# [1] "Filtering Complete: chr8_DCas20_5360_REFimputedAndFiltered"
# [1] "474 sites passing filter"
# [1] "Filtering Complete: chr9_DCas20_5360_REFimputedAndFiltered"
# [1] "243 sites passing filter"
# [1] "Filtering Complete: chr10_DCas20_5360_REFimputedAndFiltered"
# [1] "272 sites passing filter"
# [1] "Filtering Complete: chr11_DCas20_5360_REFimputedAndFiltered"
# [1] "361 sites passing filter"
# [1] "Filtering Complete: chr12_DCas20_5360_REFimputedAndFiltered"
# [1] "393 sites passing filter"
# [1] "Filtering Complete: chr13_DCas20_5360_REFimputedAndFiltered"
# [1] "755 sites passing filter"
# [1] "Filtering Complete: chr14_DCas20_5360_REFimputedAndFiltered"
# [1] "712 sites passing filter"
# [1] "Filtering Complete: chr15_DCas20_5360_REFimputedAndFiltered"
# [1] "280 sites passing filter"
# [1] "Filtering Complete: chr16_DCas20_5360_REFimputedAndFiltered"
# [1] "674 sites passing filter"
# [1] "Filtering Complete: chr17_DCas20_5360_REFimputedAndFiltered"
# [1] "610 sites passing filter"
# [1] "Filtering Complete: chr18_DCas20_5360_REFimputedAndFiltered"

Check what’s left

purrr::map(1:18,~system(paste0("zcat ",here::here("output/"),"chr",.,"_DCas20_5360_REFimputedAndFiltered.vcf.gz | wc -l")))
# 1078
# 447
# 569
# 217
# 793
# 457
# 248
# 419
# 484
# 253
# 282
# 371
# 403
# 765
# 722
# 290
# 684
# 620

cd /workdir/mw489/EMBRAPA_2020GS/output/;
cp *_DCas20_5360_REFimputedAndFiltered* /home/jj332_cas/marnin/EMBRAPA_2020GS/output/

RefPanel: Include C1, all sites

Merge RefPanel and C1

inPath<-here::here("data/")
outPath<-here::here("data/")
source(here::here("code","imputationFunctions.R"))
require(furrr); options(mc.cores=ncores); plan(multiprocess)
future_map(1:18,~mergeVCFs(inPath=inPath,
                           inVCF1=paste0("chr",.,"_ImputationReferencePanel_EMBRAPA_Phased_102619"),
                           inVCF2=paste0("chr",.,"_EMBRAPA_C1progeny_FromDCas19_4301_REFimputed_102619"),
                           outPath=outPath,
                           outName=paste0("chr",.,"_ImputationReferencePanel_C1progenyAdded_EMBRAPA")))

cd data/ 
bcftools query --list-samples chr1_ImputationReferencePanel_C1progenyAdded_EMBRAPA.vcf.gz > chr1_ImputationReferencePanel_C1progenyAdded_EMBRAPA.samples

refpanel_samples<-read.table(here::here("data","chr1_ImputationReferencePanel_C1progenyAdded_EMBRAPA.samples"), 
                             header=F, stringsAsFactors = F)$V1
target_samples<-read.table(here::here("data/Report-DCas20-5360/","DCas20_5360.samples"), 
                             header=F, stringsAsFactors = F)$V1
samplesToExclude<-target_samples[target_samples %in% refpanel_samples]
length(samplesToExclude) # [1] 713
write.table(samplesToExclude,file=here::here("data","samplesToExclude_RefPanelC1Added.txt"),
            row.names = F, col.names = F, quote = F)

Impute C2

source(here::here("code","imputationFunctions.R"))
targetVCFpath<-here::here("data/Report-DCas20-5360/") # location of the targetVCF
refVCFpath<-here::here("data/")
mapPath<-here::here("data/CassavaGeneticMap/")
outPath<-here::here("output/")
samplesToExclude<-here::here("data","samplesToExclude_RefPanelC1Added.txt")

purrr::map(1:18,~runBeagle5(targetVCF=paste0(targetVCFpath,"chr",.,"_DCas20_5360.vcf.gz"),
                            refVCF=paste0(refVCFpath,"chr",.,"_ImputationReferencePanel_C1progenyAdded_EMBRAPA.vcf.gz"),
                            mapFile=paste0(mapPath,"chr",.,"_cassava_cM_pred.v6_91019.map"),
                            outName=paste0(outPath,"chr",.,"_DCas20_5360_REFimputedWithC1unfiltered"),
                            samplesToExclude=samplesToExclude,
                            nthreads=112))

Clean up Beagle log files after run. Move to sub-directory output/BeagleLogs/.

cd /workdir/mw489/EMBRAPA_2020GS/output/; 
cp *_DCas20_5360_REFimputedWithC1unfiltered.log BeagleLogs/;
cp -r BeagleLogs /home/jj332_cas/marnin/EMBRAPA_2020GS/output/;
cp *_DCas20_5360_REFimputedWithC1unfiltered* /home/jj332_cas/marnin/EMBRAPA_2020GS/output/;

cd /workdir/mw489/EMBRAPA_2020GS/data/;
cp *_ImputationReferencePanel_C1progenyAdded_EMBRAPA* /home/jj332_cas/marnin/EMBRAPA_2020GS/data/;
cp samplesToExclude_RefPanelC1Added.txt /home/jj332_cas/marnin/EMBRAPA_2020GS/data/;

Post-impute filter

inPath<-here::here("output/")
outPath<-here::here("output/")
source(here::here("code","imputationFunctions.R"))
require(furrr); options(mc.cores=ncores); plan(multiprocess)
future_map(1:18,~postImputeFilter(inPath=inPath,
                                  inName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1unfiltered"),
                                  outPath=outPath,
                                  outName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1unfiltered_PostImputeFiltered")))

purrr::map(1:18,~system(paste0("zcat ",here::here("output/"),"chr",.,"_DCas20_5360_REFimputedWithC1unfiltered_PostImputeFiltered.vcf.gz | wc -l")))
# 1568
# 768
# 917
# 10
# 1201
# 748
# 347
# 716
# 916
# 450
# 518
# 545
# 577
# 1214
# 1179
# 406
# 1008
# 831

cd /workdir/mw489/EMBRAPA_2020GS/output/;
cp *_DCas20_5360_REFimputedWithC1unfiltered_PostImputeFiltered* /home/jj332_cas/marnin/EMBRAPA_2020GS/output/

RefPanel: Include C1, filtered sites only

Keep only the sites in the RefPanel that passed post-imputation filter for the C1

Filter sites from RefPanel+C1 dataset

inPath<-here::here("data/")
outPath<-here::here("data/")
source(here::here("code","imputationFunctions.R"))
require(furrr); options(mc.cores=18); plan(multiprocess)
furrr::future_map(1:18,~filter_positions(inPath=inPath,
                                         inVCF=paste0("chr",.,"_ImputationReferencePanel_C1progenyAdded_EMBRAPA.vcf.gz"),
                                         positionFile=paste0("chr",.,"_EMBRAPA_C1progeny_FromDCas19_4301_REFimputed_102619.sitesPassing"),
                                         outPath=outPath,
                                         outName=paste0("chr",.,"_ImputationReferencePanel_C1progenyAddedFilteredSites_EMBRAPA")))

Impute C2

source(here::here("code","imputationFunctions.R"))
targetVCFpath<-here::here("data/Report-DCas20-5360/") # location of the targetVCF
refVCFpath<-here::here("data/")
mapPath<-here::here("data/CassavaGeneticMap/")
outPath<-here::here("output/")
samplesToExclude<-here::here("data","samplesToExclude_RefPanelC1Added.txt")

purrr::map(1:18,~runBeagle5(targetVCF=paste0(targetVCFpath,"chr",.,"_DCas20_5360.vcf.gz"),
                            refVCF=paste0(refVCFpath,"chr",.,"_ImputationReferencePanel_C1progenyAddedFilteredSites_EMBRAPA.vcf.gz"),
                            mapFile=paste0(mapPath,"chr",.,"_cassava_cM_pred.v6_91019.map"),
                            outName=paste0(outPath,"chr",.,"_DCas20_5360_REFimputedWithC1filtered"),
                            samplesToExclude=samplesToExclude,
                            nthreads=112))

Clean up Beagle log files after run. Move to sub-directory output/BeagleLogs/.

cd /workdir/mw489/EMBRAPA_2020GS/output/; 
cp *_DCas20_5360_REFimputedWithC1filtered.log BeagleLogs/;
cp -r BeagleLogs /home/jj332_cas/marnin/EMBRAPA_2020GS/output/;
cp *_DCas20_5360_REFimputedWithC1filtered* /home/jj332_cas/marnin/EMBRAPA_2020GS/output/;

cd /workdir/mw489/EMBRAPA_2020GS/data/;
cp *_ImputationReferencePanel_C1progenyAddedFilteredSites_EMBRAPA* /home/jj332_cas/marnin/EMBRAPA_2020GS/data/;

Post-impute filter

inPath<-here::here("output/")
outPath<-here::here("output/")
source(here::here("code","imputationFunctions.R"))
require(furrr); options(mc.cores=ncores); plan(multiprocess)
future_map(1:18,~postImputeFilter(inPath=inPath,
                                  inName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1filtered"),
                                  outPath=outPath,
                                  outName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1filtered_PostImputeFiltered")))

Check how many sites left

purrr::map(1:18,~system(paste0("zcat ",here::here("output/"),"chr",.,"_DCas20_5360_REFimputedWithC1filtered_PostImputeFiltered.vcf.gz | wc -l")))
# 945
# 367
# 376
# 212
# 696
# 385
# 177
# 451
# 395
# 198
# 266
# 369
# 289
# 611
# 702
# 253
# 359
# 514

cd /workdir/mw489/EMBRAPA_2020GS/output/;
cp *_DCas20_5360_REFimputedWithC1filtered_PostImputeFiltered* /home/jj332_cas/marnin/EMBRAPA_2020GS/output/

sessionInfo()

Impute EMBRAPA GS C2 (DCas20_5360)

Marnin Wolfe

2020-August-26

Impute EMBRAPA GS C2

RefPanel: Exclude C1

Impute C2

Post-impute filter

RefPanel: Include C1, all sites

Merge RefPanel and C1

Impute C2

Post-impute filter

RefPanel: Include C1, filtered sites only

Filter sites from RefPanel+C1 dataset

Impute C2

Post-impute filter