VCF: removing all FORMAT but FORMAT/GT

Question

[arya.sagittarius]

how do i grep the vcf, so that i only need the GT information

Input:

chr1    67947   rs1202587463    A       AT      .       PASS    -       GT:GQ:DP:AD:MIN_DP:PGT:PID:PL:SB        0/0:22:21:.:11:.:.:.:.  0/0:24:21:.:9:.:.:.:.   0/0:2
chr1    69928   .       T       TAC     .       PASS    -       GT:GQ:DP:AD:MIN_DP:PGT:PID:PL:SB        0/0:21:22:.:8:.:.:.:.   0/0:35:34:.:21:.:.:.:.  0/0:30:18:.:1

I want the output as

chr1    67947   rs1202587463    A       AT      .       PASS    -       GT        0/0  0/0   0/0
chr1    69928   .       T       TAC     .       PASS    -       GT       0/0  0/0

I tried using sed -e 's/:.:.:.:.:.:.:.:.//g' ani.vcf but everything after GT gets eliminated

chr1    67947   rs1202587463    A       AT      .       PASS    -       GT
chr1    69928   .       T       TAC     .       PASS    -       GT

[curious]

usually I don't grep VCF if avoidable by using bcftools bcftools query my.vcf -f '[\t%GT]\n

Answer 1

[Pierre Lindenbaum]

bcftools annotate -x '^FORMAT/GT' in.vcf

[arya.sagittarius]

Thank you so much. It works ! :)

[Ram]

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Answer 2

[Istvan Albert]

Instead of regular expressions I would recommend you to use one of the many tools that allow you to filter VCF files and format the output to your needs

for example, to remove INFO tags use

bcftools annotate -x INFO/VDB,INFO/FS,INFO/SGB 

[Istvan Albert]

oh Pierre Lindenbaum solution is even better,

I forgot the exact format to use it and tested it out, hence the later answer that was not even as good as the original