Question: how to capture vcf's INFO field with bcftools
0
gravatar for genya35
18 months ago by
genya3510
genya3510 wrote:

Hello,

I'm trying to print the content of a vcf file but having problem with capturing the 'INFO' column.

Here is the code.

my $cmd2 = `bcftools query $vcf_indexed -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/TAG[\t%SAMPLE=%AD]\n' --samples '$sample'`;print $cmd2;

I get "Error: no such tag defined in the VCF header: INFO/TAG"

Thanks

software error • 917 views
ADD COMMENTlink modified 18 months ago by Pierre Lindenbaum120k • written 18 months ago by genya3510
1
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

it only works if TAG is declared in the VCF header:

grep INFO your.vcf | grep TAG

##INFO=<ID=TAG,Number=...
ADD COMMENTlink modified 18 months ago • written 18 months ago by Pierre Lindenbaum120k

Thanks, sorry for a simple question but how do I redirect the output to a text file of my choice?

Sorry, i got it. my $cmd2 = bcftools query $vcf_indexed -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/ANN][\t%SAMPLE=%AD]\n' --samples '$sample' > $output_file;print $cmd2;

ADD REPLYlink modified 18 months ago • written 18 months ago by genya3510
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 894 users visited in the last hour