Question: Recalculate QUAL and INFO fields for a subset of samples in a VCF
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gravatar for hermathena
5.0 years ago by
hermathena40
United Kingdom
hermathena40 wrote:

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

snp next-gen • 1.4k views
ADD COMMENTlink modified 5.0 years ago by geek_y11k • written 5.0 years ago by hermathena40

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?

ADD REPLYlink modified 12 months ago by _r_am32k • written 5.0 years ago by Sean Davis26k

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

ADD REPLYlink written 5.0 years ago by lh332k

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

Which version of bcftools, please?

ADD REPLYlink written 5.0 years ago by hermathena40

what is the command?

ADD REPLYlink written 2.7 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
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