Taking genotypes out of a vcf file

Question

[Jautis]

Hi, I would like to take a vcf file and output a tab-delimited file with a line per individual-site that includes the individual, site, GT, alternate and reference alleles, DP, and each PL. It doesn't matter what order sites end up being in.

Any suggestions on how to do this most efficiently and/or any links to code that does something like this?

Example input:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  samp1 samp2
chr1   100  .       C       T       3106.72 SnpCluster      .       GT:AD:DP:GQ:PL  0/0:1,0:1:3:0,3,42      0/0:3,0:3:9:0,9,132
chr1   120  .       C       G       3106.72 SnpCluster      .       GT:AD:DP:GQ:PL 0/1:3,1:4:30:30,0,123   1/1:0,1:1:3:45,3,0

Example output:

samp1    chr1    100    0/0   C   T   1    0   3   42
samp2    chr1    100   0/1    C   T   4   30   0   123
samp1    chr1    120    0/0   C   G   3    0    9    132
samp2    chr1    120    1/1   C   G   1    45   3    0

[ethan.kaufman]

If you're into python, pyvcf makes this sort of task quite easy.

Answer 1

[Pierre Lindenbaum]

Using my tool Bioalcidae: https://github.com/lindenb/jvarkit/wiki/BioAlcidae

file format.js

while(iter.hasNext())
    {
    var ctx = iter.next();
    for(var I = 0;i< ctx.getNSamples();++i)
        {
        var g = ctx.getGenotype(i);
        out.print(g.getSampleName());
        out.print("\t");
        out.print(ctx.contig);
        out.print("\t");
        out.print(ctx.start);
        out.print("\t");
        if(g.isCalled())
            {
            out.print(ctx.getAlleleIndex(g.getAllele(0))+"/"+ctx.getAlleleIndex(g.getAllele(1)));
            out.print("\t");
            out.print(g.getAllele(0).getDisplayString());
            out.print("\t");
            out.print(g.getAllele(1).getDisplayString());
            }
        else
            {
            out.print(".\t.\t.");
            }
        out.print("\t");
        out.print(g.getDP());
        out.print("\t");
        out.print(g.getGQ());
        out.print("\t");
        out.print(g.getAnyAttribute("NR"));
        out.println();
        }
    }

Invoke:

curl -sL "https://raw.githubusercontent.com/KBoehme/VTCTesting/master/src/test/resources/test_data/UnionTests/Test4/input2.vcf" | java -jar dist-1.133/bioalcidae.jar -F VCF -f format.js

Result:

NA00001    chr1    1451489    0/0    T    T    -1    35    18
NA00002    chr1    1451489    1/0    C    T    -1    100    24
NA00001    chr1    1451490    0/0    G    G    -1    35    18
NA00002    chr1    1451490    0/1    G    A    -1    100    24
NA00001    chr1    12939904    0/0    A    A    -1    45    53
NA00002    chr1    12939904    0/1    A    C    -1    100    79
NA00001    chr1    16902943    0/0    T    T    -1    26    93
NA00002    chr1    16902943    0/1    T    C    -1    84    98
NA00001    chr1    16902982    0/0    G    G    -1    52    108
NA00002    chr1    16902982    0/1    G    T    -1    75    115
(...)

[Jautis]

Thank you very much! That seems perfect. However, I'm having difficulties getting a working copy of bioalcidae.jar. When I download the .jar file, I get an error message saying it is invalid or corrupt. Is there anything else I need to do?

[Pierre Lindenbaum]

(?!) there is no jar fileto download, you need to install and compile the program ;

git clone "https://github.com/lindenb/jvarkit.git" && cd jvarkit &&  make bioalcidae && java -jar dist-1.133/bioalcidae.jar -h

[Jautis]

Oh, thank you. I feel like an idiot now

Answer 2

[Matt Shirley]

I'm partial to the vawk tool. It's simple, but gets the job done quickly.