Last updated: 2020-10-17
Checks: 7 0
Knit directory: EMBRAPA_2020GS/
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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/ImputeDCas20_5360.Rmd) and HTML (docs/ImputeDCas20_5360.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 |
|---|---|---|---|---|
| Rmd | d2fd3f7 | wolfemd | 2020-10-17 | Add a ‘lightly-filtered’ version of the dataset. Create genome-wide |
| html | 7e4c8ad | wolfemd | 2020-09-01 | Build site. |
| Rmd | f15718e | wolfemd | 2020-09-01 | wflow_publish(c(“analysis/ImputeDCas20_5360.Rmd”)) |
| html | d29d605 | wolfemd | 2020-09-01 | Build site. |
| 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):
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.
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/ 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.samplesrefpanel_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)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/.
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
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.samplesrefpanel_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)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/;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 <--- ZERO MARKERS ON CHR. 4 (10 ROWS = THE HEADER)
# 1201
# 748
# 347
# 716
# 916
# 450
# 518
# 545
# 577
# 1214
# 1179
# 406
# 1008
# 831Keep only the sites in the RefPanel that passed post-imputation filter for the C1
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")))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/;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
inPath<-here::here("output/")
outPath<-here::here("output/")
source(here::here("code","imputationFunctions.R"))
require(furrr); options(mc.cores=18); plan(multiprocess)
# Re-filter the REFimputed dataset
future_map(1:18,~postImputeFilter(inPath=inPath,
inName=paste0("chr",.,"_DCas20_5360_REFimputed"),
outPath=outPath,
outName=paste0("chr",.,"_DCas20_5360_REFimputeLightFiltDR2pt3"),
DR2thresh=0.3))
# Re-filter the REFimputedWithC1unfiltered dataset
future_map(1:18,~postImputeFilter(inPath=inPath,
inName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1unfiltered"),
outPath=outPath,
outName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1unfiltered_LightPostImputeFiltDR2pt3"),
DR2thresh=0.3))
# Re-filter the REFimputedWithC1filtered dataset
future_map(1:18,~postImputeFilter(inPath=inPath,
inName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1filtered"),
outPath=outPath,
outName=paste0("chr",.,"_DCas20_5360_REFimputedWithC1filtered_LightPostImputeFiltDR2pt3"),
DR2thresh=0.3))
# Check what's left
## REFimputed dataset
purrr::map(1:18,~system(paste0("zcat ",here::here("output/"),"chr",.,"_DCas20_5360_REFimputeLightFiltDR2pt3.vcf.gz | wc -l")))
# 2399
# 1443
# 1714
# 554 <---- THAT'S BETTER THAN BELOW
# 1966
# 1319
# 618
# 1176
# 1417
# 965
# 866
# 1082
# 1019
# 1850
# 1867
# 746
# 1812
# 1347
## REFimputedWithC1unfiltered dataset
purrr::map(1:18,~system(paste0("zcat ",here::here("output/"),"chr",.,"_DCas20_5360_REFimputedWithC1unfiltered_LightPostImputeFiltDR2pt3.vcf.gz | wc -l")))
# 2735
# 1722
# 1845
# 10 <---- THAT'S NOT GOOD. ZERO CHR. 4 MARKERS
# 2154
# 1574
# 836
# 1349
# 1563
# 1327
# 1056
# 1243
# 1149
# 2006
# 1993
# 879
# 1948
# 1530
## REFimputedWithC1filtered dataset
purrr::map(1:18,~system(paste0("zcat ",here::here("output/"),"chr",.,"_DCas20_5360_REFimputedWithC1filtered_LightPostImputeFiltDR2pt3.vcf.gz | wc -l")))
# 970
# 416
# 406
# 228
# 755
# 396
# 179
# 487
# 405
# 222
# 274
# 394
# 316
# 697
# 733
# 259
# 382
# 552The function below will (1) convert the input VCF to plink1.9 binary format and (2) convert the plink binary to a dosage (0,1,2) matrix with special attention to which allele gets counted in the file.
NOTICE: I was worried about plink1.9 changing allele codes between files. There is some risk the counted allele could switch between e.g. the reference panel and the progeny files because of allele freq. (see plink documentation). To avoid this, went to extra trouble: write a file suffixed *.alleleToCount listing SNP ID (column 1) and the ALT allele from the VCF (column 2). Pass the file to plink1.9 using the --recode-allele flag to ensure all output dosages count the ALT allele consistent with the VCFs. The reason to use plink1.9 is that Beagle5 imputed files don’t have a DS (dosage) field that can be directly extracted. Instead, phased genotypes e.g. 0|1 need to be converted to dosages (e.g. 0|1 --> 1, 1|1 --> 2). An alternative might be to extract the haplotypes using vcftools and manually (in R) computed the dosages; that would give most control but is slow.
library(tidyverse); library(magrittr);
source(here::here("code","imputationFunctions.R"))
require(furrr); options(mc.cores=18); plan(multiprocess)
pathOut<-here::here("output/")
# 9 different filesets to convert
## Imputation reference panels
future_map(1:18,~convertVCFtoDosage(pathIn="/home/jj332_cas/CassavaGenotypeData/nextgenImputation2019/ImputationEMBRAPA_102419/",
pathOut=pathOut,
vcfName = paste0("chr",.,"_ImputationReferencePanel_EMBRAPA_Phased_102619")))
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("data/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_ImputationReferencePanel_C1progenyAdded_EMBRAPA")))
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("data/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_ImputationReferencePanel_C1progenyAddedFilteredSites_EMBRAPA")))
## Standard filtered imputed C2
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("output/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_DCas20_5360_REFimputedAndFiltered")))
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("output/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_DCas20_5360_REFimputedWithC1unfiltered_PostImputeFiltered")))
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("output/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_DCas20_5360_REFimputedWithC1filtered_PostImputeFiltered")))
## "Lightly" filtered imputed C2
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("output/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_DCas20_5360_REFimputedWithC1filtered_LightPostImputeFiltDR2pt3")))
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("output/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_DCas20_5360_REFimputedWithC1unfiltered_LightPostImputeFiltDR2pt3")))
future_map(1:18,~convertVCFtoDosage(pathIn=here::here("output/"),pathOut=pathOut,
vcfName = paste0("chr",.,"_DCas20_5360_REFimputeLightFiltDR2pt3")))
# Genome-wide dosage (for use in R) for each dataset
## Imputation reference panels
createGenomewideDosage(pathIn = here::here("output/"), chroms=1:18, "_ImputationReferencePanel_EMBRAPA_Phased_102619")
createGenomewideDosage(pathIn = here::here("output/"), chroms=1:18, "_ImputationReferencePanel_C1progenyAdded_EMBRAPA")
createGenomewideDosage(pathIn = here::here("output/"), chroms=1:18, "_ImputationReferencePanel_C1progenyAddedFilteredSites_EMBRAPA")
## Standard filtered imputed C2
createGenomewideDosage(pathIn = here::here("output/"), chroms=1:18, "_DCas20_5360_REFimputedAndFiltered")
createGenomewideDosage(pathIn = here::here("output/"), chroms=c(1:3,5:18), # chrom 4 missing from this one
"_DCas20_5360_REFimputedWithC1unfiltered_PostImputeFiltered")
createGenomewideDosage(pathIn = here::here("output/"), chroms=1:18, "_DCas20_5360_REFimputedWithC1filtered_PostImputeFiltered")
## "Lightly" filtered imputed C2
createGenomewideDosage(pathIn = here::here("output/"), chroms=1:18, "_DCas20_5360_REFimputedWithC1filtered_LightPostImputeFiltDR2pt3")
createGenomewideDosage(pathIn = here::here("output/"), chroms=c(1:3,5:18), # chrom 4 missing from this one
"_DCas20_5360_REFimputedWithC1unfiltered_LightPostImputeFiltDR2pt3")
createGenomewideDosage(pathIn = here::here("output/"), chroms=1:18, "_DCas20_5360_REFimputeLightFiltDR2pt3")