Last updated: 2020-09-01
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Knit directory: EMBRAPA_2020GS/
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library(tidyverse); library(magrittr)
dartvcfInput<-paste0("/workdir/marnin/DCas19_4403/Report_4403_VCF_Version_6.csv")
dartcountsInput<-paste0("/workdir/marnin/DCas19_4403/Report_4403_Counts_Version_6_updated.csv")
outName<-paste0("/workdir/marnin/DCas19_4403/DCas19_4403_102419")
nskipvcf<-2
nskipcounts<-3
ncores<-75 # using more than a few could be VERY memory intensive# convertDart2vcf<-function(dartvcfInput,dartcountsInput,outName,
# nskipvcf=2,nskipcounts=3,ncores){
#rm(vcf,readCounts); gc()
vcf<-read.table(dartvcfInput,
stringsAsFactors = F,skip = nskipvcf, header = T, sep = "\t", comment.char = "")
dim(vcf) # [1] 13603 654
readCounts<-read.csv(dartcountsInput, stringsAsFactors = F,header = T,skip=nskipcounts)
colnames(vcf)[10:length(colnames(vcf))]<-colnames(readCounts)[43:length(colnames(readCounts))]
vcf %<>%
mutate(X.CHROM=gsub("Chromosome","",X.CHROM)) %>%
rename(Pos=POS) %>%
mutate(Chr=as.numeric(gsub("Chromosome","",X.CHROM)),
Pos=as.numeric(Pos))
# dim(readCounts)
# readCounts %>% .[,1:30] %>% str
# readCounts[1:5,1:30]
# readCounts[1:10,] %>% select(SNP,CloneID,AlleleID,Chrom_Cassava_v61,SNP_ChromPos_Cassava_v61)
# vcf[1:10,1:5]
# Note: The ID column in "vcf" is the value for the ALT allele in AlleleID of "readCounts"
readCounts %<>%
mutate(RefAlt=ifelse(SNP=="","REF","ALT"),
Chr=as.numeric(gsub("Chromosome","",Chrom_Cassava_v61)),
Pos=as.numeric(SNP_ChromPos_Cassava_v61))Add a unique value “SNPindex” to each SNP in the vcf and readCounts df’s For readCounts, this is going to be the best way to keep track of pairs of rows. Since in many cases, multiple CloneID can point to same Chr-Pos-Alleles and it’s otherwise unclear which pair of rows should go together when subsetting downstream.
dim(vcf) # [1] 13603 655
dim(readCounts) # [1] 27206 690
vcf %<>%
mutate(SNPindex=1:nrow(.))
readCounts %<>%
mutate(SNPindex=sort(rep(1:(nrow(.)/2),2)))readCounts %<>%
separate(AlleleID,c("tmp","Alleles"),sep=-3,remove = F) %>%
select(-tmp) %>%
separate(Alleles,c("REF","ALT"),">",remove = F)
vcf %<>%
separate(ID,c("tmp","Alleles"),sep=-3,remove = F) %>%
select(-tmp)
vcf %<>%
separate(ID,c("CloneID","tmp"),"[|]",remove = F,extra = 'merge') %>%
mutate(CloneID=as.numeric(CloneID)) %>%
select(-tmp) %>%
rename(AlleleID=ID)# Add required VCF fields
## First have to do some data transformation and
## create some of the meta-data fields in a VCF, e.g. QUAL, FILTER INFO.
readCounts %<>%
arrange(Chr,Pos,SNPindex,CloneID,AlleleID,RefAlt) %>%
mutate(QUAL=".",
FILTER=".",
INFO=".",
FORMAT="GT:AD:DP:PL",
SNP_ID=paste0("S",Chr,"_",Pos))
vcf %<>%
arrange(Chr,Pos,SNPindex,CloneID,AlleleID) %>%
mutate(QUAL=".",
FILTER=".",
INFO=".",
FORMAT="GT:AD:DP:PL",
SNP_ID=paste0("S",Chr,"_",Pos))
vcf %>%
select(Chr,Pos,SNPindex,CloneID,AlleleID,Alleles,REF,ALT,QUAL,FILTER,INFO,FORMAT,SNP_ID) %>% head
readCounts %>% filter(RefAlt=="ALT") %>%
select(Chr,Pos,SNPindex,CloneID,AlleleID,Alleles) %>% slice(1:10)sites2keep<-vcf %>%
count(Chr,Pos) %>%
ungroup() %>%
filter(n==1) %>%
select(-n) %>%
semi_join(
readCounts %>%
count(Chr,Pos) %>%
arrange(desc(n)) %>%
filter(n==2) %>%
select(-n)) # 12049 sites
vcf %<>% semi_join(sites2keep)
readCounts %<>% semi_join(sites2keep)table((readCounts %>% filter(RefAlt=="ALT") %$% SNPindex)==vcf$SNPindex)
sampleIDsFromDartVCF<-colnames(vcf) %>%
.[!. %in% c("X.CHROM","Pos","AlleleID","Alleles","REF","ALT","QUAL","FILTER","INFO","FORMAT",
"Chr","SNPindex","CloneID","SNP_ID","SNP")]
head(sampleIDsFromDartVCF); tail(sampleIDsFromDartVCF)
tmp_counts <-readCounts %>%
.[,c("Chr","Pos","SNPindex","SNP_ID",
"CloneID","AlleleID","RefAlt","Alleles","QUAL","FILTER","INFO","FORMAT",sampleIDsFromDartVCF)] %>%
semi_join(sites2keep)
dim(tmp_counts) # [1] 24098 657
tmp_counts %<>%
gather(FullSampleName,ReadCount,sampleIDsFromDartVCF)
dim(tmp_counts) # [1] 15543210 14
tmp_counts %<>%
select(-AlleleID) %>%
spread(RefAlt,ReadCount)
dim(tmp_counts) # [1] 7771605 13
head(tmp_counts)
tmp_counts %<>%
rename(AltCount=ALT,
RefCount=REF)
dim(tmp_counts) # [1] 7771605 13
vcf_long<-vcf %>%
.[,c("Chr","Pos","SNPindex","SNP_ID",
"CloneID","Alleles","REF","ALT","QUAL","FILTER","INFO","FORMAT",sampleIDsFromDartVCF)] %>%
gather(FullSampleName,GT,sampleIDsFromDartVCF)
dim(vcf_long) # [1] 7771605 14
table(vcf_long$CloneID %in% tmp_counts$CloneID) # all trueI use the DArT genotype call (GT) for the PLINK IBD step.
PLINK requires genotype calls.
Later, I impute in GL mode, so GTs are ignored.
# AD+DP fields
## Now we can calc DP and formate the VCF field "AD" (e.g. "21,0" for 21 reference reads and 0 alt. allele reads)
tmp_counts %<>%
mutate(DP=AltCount+RefCount,
AD=paste0(RefCount,",",AltCount))
tmp1<-tmp_counts %>%
filter(!is.na(AltCount),
!is.na(RefCount))
tmp<-tmp1; rm(tmp1)
tmp %>% head
# Calc. genotype likelihoods
## Genotype likelihoods calculated according to:
### http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862#s4
## Converted to Normalized Phred Scores according to:
### https://gatkforums.broadinstitute.org/gatk/discussion/5913/math-notes-how-pl-is-calculated-in-haplotypecaller
## Truncate low Phred probabilities (high Phred scores) to
### 255 max according to TASSEL's convention (Jeff Glaubitz, pers. communication).
#ref<-171; alt<-171; error<-0.001
calcPL<-function(ref,alt,error=0.001){
# ref and alt arguments are read counts for ref and alt allele, repsectively
dp<-ref+alt
# for values >170, factorial() returns 'inf'
# Since it means essentially 100% probability of a genotype...
# set DP to 169 cieling, ref/alt to equiv. allele proportions
if(dp>=170){ ref<-169*(ref/dp); alt<-169*(alt/dp); dp<-169 }
gl_RefRef<-(factorial(dp)/(factorial(ref)*factorial(alt)))*(1-(0.75*error))^ref*(error/4)^(alt)
gl_RefAlt<-(factorial(dp)/(factorial(ref)*factorial(alt)))*(0.5-(0.25*error))^(ref+alt)*(error/4)^(0)
gl_AltAlt<-(factorial(dp)/(factorial(ref)*factorial(alt)))*(1-(0.75*error))^alt*(error/4)^(ref)
phredScale<--10*log10(c(gl_RefRef,gl_RefAlt,gl_AltAlt))
minPhred<-min(phredScale)
normPhred<-round(phredScale-minPhred,0)
normPhred[which(normPhred>=255)]<-255
normPhred<-paste0(normPhred,collapse = ",")
if(dp==0){ normPhred<-"." }
return(normPhred)
}
require(furrr); options(mc.cores=ncores); plan(multiprocess)
tmp %<>%
mutate(PL=future_map2_chr(RefCount,AltCount,~calcPL(ref=.x,alt=.y)))
tmp %>% head
dim(tmp) # [1] 7771605 19header<-c("##fileformat=VCFv4.0",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
"##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the reference and alternate alleles in the order listed\">",
"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth (only filtered reads used for calling)\">",
"##FORMAT=<ID=PL,Number=3,Type=Float,Description=\"Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic\">")options("scipen"=1000, "digits"=4)
# for a few SNPs, position kept printing in sci notation e.g. 1e3, screws up Beagle etc., this avoids that (I hope)
write_lines(header,
path=paste0(outName,".vcf"))
write.table(tmp,
paste0(outName,".vcf"),
append = T,sep = "\t",row.names=F, col.names=T, quote=F)
# Save sitesWithAlleles
tmp %>%
rename(CHROM=`#CHROM`) %>%
select(CHROM:ALT) %>%
write.table(.,file=paste0(outName,".sitesWithAlleles"),
row.names=F)
# Save sample list
write.table(sampleIDsFromDartVCF,file=paste0(outName,".samples"),
row.names = F, col.names = F, quote = F)
# BGzip
system(paste0("cat ",outName,".vcf ",
"| bgzip -c > ",outName,".vcf.gz"))
system(paste0("rm ",outName,".vcf"))