Would it be possible to have vcffixup also output the DP INFO field?

[WimS83]

Hi,

Would it be possible to have vcffixup also output the DP INFO field?

After pre-processing a vcf file with vcfallelicprimitives and vcffixup, the DP field is missing from the variants that were converted to allelic primitives.

Currently allelicprimitives drops all INFO fields and vcffixup only recalculates AC, AF, AN, LEN and NS.

We depend on the DP INFO field downstream and would like to have it present for all variants , including the ones split by allelic primitives. The DP field is still present for the genotypes, so it should be possible to recalculate the DP INFO field?

Thanks!

[zeeev]

DP can be tricky. Do you just want the sum of the genotype DPs?

[NeillGibson]

We downstream calculate the sum of the genotype depths now in the case of a missing variant depth.

It could still be useful to have this functionality with an optional argument in vcffixup .

[zeeev]

@NeillGibson I'll add that feature in the next couple days. Thanks for the suggestions.