Recalculate QUAL and INFO fields for a subset of samples in a VCF

Question

[hermathena]

Dear All,

I extracted some samples from a larger VCF (one population of a species). I would like to filter the sites by quality and depth. However, the values in the new VCF still seem to reflect the data from the bigger VCF (i.e. the average depth was calculated for all samples, not just the extracted ones). Do any of the usual tools (GATK, bcftools, etc) offer a way of recalculating site quality or the INFO fields for the current subset of samples?

Many thanks

[Sean Davis]

Besides the issue of "software that can do that", there is the issue of whether the data to do so are supplied with the VCF samples. What format fields are present for the genotype records?

[lh3]

If you have GL/PL, some versions of bcftools can do this.

[hermathena]

Indeed, the FORMAT fields available are AB, AD, DP, GQ, GT, MQ0, PL.

Which version of bcftools, please?

[QVINTVS_FABIVS_MAXIMVS]

what is the command?