Extract several fields from vcf file

Question

[kelly.wang135]

Hello all, I'd like to modify my vcfs to contain several info only. There are "GT:AD:DP:FT:GQ:PL:PP" in format column, but I want to include "GT,DP,GQ" only.

I ran "--extract-FORMAT-info" of vcftools, but the result file is not vcf format. What I want to have finally, is vcf file with "GT,DP,GQ" fields only.

Does anyone know how to handle this? Thanks.

[Benn]

Have you tried AWK aleady?

[kelly.wang135]

Actually I extracted these fields with python. But when I tried to analyze this file using rare variant association tool like pseq, vtools, and rvtest, something is not working properly.

I wonder it there are validated tools to extract, not with linux or python.

[lakhujanivijay]

Can you please provide a line having GT:AD:DP:FT:GQ:PL:PP from the vcf file?

[kelly.wang135]

Thanks, but I am looking for tools to handle this.

[ziv_attia]

you can use bcftools annotate to keep/remove FORMAT fields

Answer 1

[Len Trigg]

Using RTG Tools:

rtg vcfsubset -i input.vcf.gz -o output.vcf.gz --keep-format GT,DP,GQ

Answer 2

[erdiazval]

I would go for using SNPSift program This is an instance of how I use it to extract: position, ref allele, alt allele, Allele Depth (AD from genotype field), and functional annotation by gene ID.

!/bin/bash
for i in *.vcf;
do java -jar /data/software/snpEff/snpEff/SnpSift.jar\
extractFields "$i"\
POS REF ALT GEN[*].AD ANN[*].GENEID > "filt_${i}";
done

Answer 3

[nsmi8446]

Have you come across SnpSift in your search for tools to do this?

http://snpeff.sourceforge.net/SnpSift.html

Section 10 in the link above (SnpSift documentation) could potentially be useful: 10. SnpSift Extract Fields