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how to capture vcf's INFO field with bcftools

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
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by genya35 • genya35

1 answer

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

grep INFO your.vcf | grep TAG

##INFO=<ID=TAG,Number=...
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written by Pierre Lindenbaum Pierre Lindenbaum

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;

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written by genya35 • genya35

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