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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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split-vep AF #2279

Closed andrew2k closed 2 months ago

andrew2k commented 2 months ago

Dear Bcftools team,

I am trying to use the +split-vep plugin in order to parse a VEP vcd file (bcftools 1.19). The plugin seems to work well, but I often don't get any value in the AF column. Have you any idea why ?

This is the command I used: bcftools +split-vep vep_output.ann.vcf.gz -f '\t%CHROM\t%ID\t%POS\t%REF\t%ALT\t%CSQ[\t%GT][\t%GQ][\t%DP][\t%AD][\t%PL]\n' -H -d -A tab > output_vep.tsv

Thx a million.

pd3 commented 2 months ago

The question is confusing, the +split-vep command you show does not request the AF values to be printed. Assuming it is just a typo, the question still cannot be answered without seeing the VCF. The most likely explanation is that the variants in the VCF don't have the AF values filled in...?