FORMAT fields

[Sirisha]

Hi,

Is there any way to use vcfanno to modify the 'FORMAT' fields? I have some exome VCFs which colleagues would like to filter/annotate in another software package. This package can't bring in ExAC frequencies, so I've used vcfanno to bring these in to the VCF. This was pretty straightforward, but the software can only detect the allele frequency if it's encoded as part of the 'FORMAT' string, so e.g:

GT:GQ:GQX:DP:DPF:AD:VF    0/1:48:14:11:2:9,2:0.2553

where VF is the calculated allele frequency in ExAC. Currently, after using vcfanno, this appears as VF=0.2553 in the INFO column, but I need it to also appear in the FORMAT column.

Thanks you :)

[Brent Pedersen]

Hi, vcfanno will only annotate the INFO, not the FORMAT. You can
filter based on the INFO with bcftools.
-Brent

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[Sirisha]

Hi,

Thanks for this - I'll use bcftools in that case,

Sirisha