Convert VCF 012 format to raw genotype data

Question

[mike1234]

I would like to convert unphased VCF genotypes into raw genotype data. For example if my REF is C and ALT is T, I would convert 0/0 to CC, 0/1 to CT, 1/0 to TC and 1/1 to TT. Bonus question: Would it also be possible to convert both 0/1 and 1/0 to the same CT instead of converting 1/0 to TC. Does vcftools do this? Possibly another tool? Thanks for your help.

Answer 1

[Pierre Lindenbaum]

using bioalcidae:

while(iter.hasNext())
    {
    var ctx= iter.next();
    out.print(ctx.getContig());
    out.print("\t");
    out.print(ctx.getStart());
    for(var i=0;i< ctx.getNSamples();++i)
        {
        out.print("\t");
        var g=ctx.getGenotype(i);
        if(g.isNoCall()) 
            {
            out.print("-");
            }
        else
            {
            var alleles=[];
            for(var k=0;k< g.getAlleles().size();++k)
                {
                alleles.push(g.getAlleles().get(k).getDisplayString());
                }
            alleles.sort();
            out.print(alleles.join("/"));
            }
        }
    out.println();
    }

example:

$ java -jar dist/bioalcidae.jar -f script.js input.vcf

rotavirus   51  A/A A/A A/A G/G
rotavirus   91  A/A A/T A/A A/A
rotavirus   130 C/T T/T T/T T/T
rotavirus   232 A/T T/T T/T T/T
rotavirus   267 C/G C/C C/C C/C
rotavirus   424 A/A A/G A/A A/A
rotavirus   520 T/T T/T A/T T/T
rotavirus   536 T/T A/A A/A A/A
rotavirus   562 A/A A/A A/A A/G
rotavirus   583 G/G G/G G/G C/G
rotavirus   661 T/T A/T T/T T/T
rotavirus   693 G/G T/T T/T T/T
rotavirus   738 T/T T/T A/T T/T
rotavirus   799 A/A A/A C/C A/A
rotavirus   812 G/G G/G T/T G/G
rotavirus   833 A/A G/G G/G G/G
rotavirus   916 T/T A/A A/A A/A
rotavirus   946 C/C A/C C/C C/C
rotavirus   961 A/T T/T T/T T/T
rotavirus   1044    A/A T/T A/A A/A
rotavirus   1045    C/C C/C G/G C/C
rotavirus   1054    C/C G/G C/C C/C
rotavirus   1064    G/G G/G G/G A/A

[mmyoussef10]

Hi Pierre Lindenbaum, Thanks a lot for the script. When I am running the script on file like this one down, it gives error. Any suggesstion how the script could be modified to work also with this format? Thanks

#CHROM  POS REF ALT QUAL    FILTER  INFO    FORMAT  atcc2355    cd01    cd02    cd03    cd04    cd05
atcc2355    530 T   C   40  PASS    NA  GT  0   0   0   0   0   0   0   0   
atcc2355    531 A   T   40  PASS    NA  GT  0   0   0   0   0   0   0   0
atcc2355    533 A   C,T 40  PASS    NA  GT  0   0   1   2   0   0   0   0
atcc2355    569 G   A   40  PASS    NA  GT  0   0   0   0   0   0   0   0
atcc2355    573 T   C,A 40  PASS    NA  GT  0   1   1   1   1   1   2   1
atcc2355    599 A   G   40  PASS    NA  GT  0   0   0   0   0   0   0   0