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?