Last updated: 2020-10-17

Checks: 7 0

Knit directory: EMBRAPA_2020GS/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


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The results in this page were generated with repository version d2fd3f7. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


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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):

  1. Last year’s reference panel, without C1 (64K SNP)
  2. Last year’s reference panel + C1 (reduce refpanel to sites passing post-impute filter in C1 = 9K SNP)
  3. 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 <--- ZERO MARKERS ON CHR. 4 (10 ROWS = THE HEADER)
# 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/

Lighter post-impute filters

cd /home/jj332_cas/marnin/EMBRAPA_2020GS;
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
# 552
cd /workdir/mw489/EMBRAPA_2020GS/output/;
cp *_DCas20_5360_REFimputedAndFiltered* /home/jj332_cas/marnin/EMBRAPA_2020GS/output/

Formats for downstream analysis

The 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.

cd /home/jj332_cas/marnin/EMBRAPA_2020GS/;
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")

sessionInfo()