What's the recommended way to create population-level Allele Frequency variant entries from a set of individuals (vcfs?) in the 1000 genomes (or similar) project?
For example, given the IBS individuals in the 1000 Genomes project:
I would like to create an IBS
.vcf.gz that contains an IBS population-level AF entry for each of the variants present.
Any ideas on how to achieve this?
EDIT: this is related to my earlier question on how to create the most complete file for population allele frequencies, here: what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?
I have seen that there is an Allele Frequency Calculator tool in EnsEMBL, which is at least available with GRCh37:
There are also instructions on how to do this genome-wide using vcftools:
vcf-subset -c ~/1000g/IBS.samples.list ~/1000g/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz | fill-an-ac | bgzip -c > ~/1000g/IBS.chr1.20130502.vcf.gz
This seems to be generating correct files, and the AF can be calculated with a tool that combines
AN values, such as it is described here:
Any other ideas / warnings / pitfalls of the approach?