swap genotypes for specific fields of a vcf file

Question

Is there a tool already established to "swap" the ref/alt information in the GT, AD and PL fields of a vcf file?

For the GT field, I need to transform: 0/0 -> 1/1 ; 1/1 -> 0/0 ; 0/1 -> 1/0 ; and finally 1/0 -> 0/1

For the AD field, I need to swap the columns: x,y -> y,x

For the PL field, I need to swap the columns: x,y,z -> z,y,x

Sample input:

Contig111   11  Contig111_11_T_G    T   G   4278.22 PASS    AC=8;AF=0.073;AN=110;BaseQRankSum=1.35;DP=1176;ExcessHet=0.1448;FS=1.841;InbreedingCoeff=0.1904;QD=13.41;ReadPosRankSum=0.351;set=Intersection  GT:AD:DP:GQ:PL  0/0:17,0:17:48:0,48,720 0/1:14,8:22:99:167,0,347 .....

Sample output:

    Contig111   11  Contig111_11_T_G    T   G   4278.22 PASS    AC=8;AF=0.073;AN=110;BaseQRankSum=1.35;DP=1176;ExcessHet=0.1448;FS=1.841;InbreedingCoeff=0.1904;QD=13.41;ReadPosRankSum=0.351;set=Intersection  GT:AD:DP:GQ:PL  1/1:0,17:17:48:720,48,0 1/0:8,14:22:99:347,0,167 .....

note: the same operations will need to be carried out for all samples if the VCF file has multiple samples (the ... stand for other potential samples).

Before I dive into scripting ( basically playing with regex), I would like to know if something to process this is already available. I looked into bcftools and fixref but they don't seem to help for this.

Answer 1

If we can always assume your fields will be GT:AD:DP:GQ:PL, you can use this relatively simple, brute approach awk script:

awk -vOFS="\t" -F"\t" '{
  ## just print the header lines
  if(/^#/){
    print;
  }
  else{    
    ## The number of samples will be the extra number of fields 
    ## in addition to the default VCF 9
    sampleNum = NF - 9
    ## Fix each sample
    for(i=1; i<=sampleNum; i++){
      ## get the fields
      num=split($(9+i), fields,":");
      ## genotype
      if(fields[1] ~ "0/0"){ fields[1] = "1/1"}
      else if(fields[1] == "1/1"){ fields[1] = "0/0" }
      else if(fields[1] == "0/1"){ fields[1] = "1/0" }
      else if(fields[1] == "1/0"){ fields[1] = "0/1" }
      ## AD
      split(fields[2],values,",")
      fields[2] = values[2]","values[1]
      ## PL
      split(fields[2],values,",")
      ## Now set these as the sample data
      $(9+i) = fields[1];
      for(k=2;k<=num;k++){
        $(9+i) = $(9+i)":"fields[k]
      }
    }
    print;
  }
}' file.vcf

On your example input, this returns:

Contig111   11  Contig111_11_T_G    T   G   4278.22 PASS    AC=8;AF=0.073;AN=110;BaseQRankSum=1.35;DP=1176;ExcessHet=0.1448;FS=1.841;InbreedingCoeff=0.1904;QD=13.41;ReadPosRankSum=0.351;set=Intersection  GT:AD:DP:GQ:PL  1/1:0,17:17:48:0,48,720 1/0:8,14:22:99:167,0,347    .....