This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Pulling out "alts" from a multisample vcf by sample ID - bcftools syntax question

Dear Biostars,

I have a multisample vcf. I would like a to turn this into a per sample "alts" file as below.

The desired outcome would be :

chr10:12342:A:T  SAMPLEID1:0/1 SAMPLEID2:1/1 ...
chr10:432234:G:C SAMPLEID4:0/1 SAMPLEID7:1/1 ...

I have tried :

bcftools query -f "%CHROM:%POS:%REF:%ALT\n[%SAMPLE:%GT\t]'  i- 'GT="alt"' input.vcf

which gives me:

chr10:12342:A:T  SAMPLEID1:0/1 SAMPLEID2:1/1 chr10:432234:G:C 
SAMPLEID4:0/1 SAMPLEID7:1/1 ...

or

 bcftools query -f "%CHROM:%POS:%REF:%ALT\t[%SAMPLE:%GT\n']  i- 'GT="alt"' input.vcf 


chr10:12342:A:T  SAMPLEID1:0/1 
SAMPLEID2:1/1 
chr10:432234:G:C SAMPLEID4:0/1 
SAMPLEID7:1/1

or

  bcftools query -f "%CHROM:%POS:%REF:%ALT\t[%SAMPLE:%GT\t']  i- 'GT="alt"' input.vcf 

  chr10:12342:A:T  SAMPLEID1:0/1 SAMPLEID2:1/1 chr10:432234:G:C SAMPLEID4:0/1 SAMPLEID7:1/1

I can't quite get my head around the correct syntax and sure there is an easy fix! Your help would be much appreciated.

All the best

bcftools vcf
• 1,027 views • link
written by tacrolimus tacrolimus

1 answer

Figured it out!

bcftools query -f "%CHROM:%POS:%REF:%ALT[\t%SAMPLE:%GT]\n'  i- 'GT="alt"' input.vcf

Just needed to move the \n out of the square brackets!

• 0 views • link
written by tacrolimus tacrolimus

Log in to answer this question.

More posts like this