Alt allele count from 1000 genome project

Question

[seta]

Hi all,

I would like to compare the Alt allele frequency of a list of thousands SNPs derived from my project with the various populations of 1000 genome project. So, I need alt allele count, could you please help me out how to find this infromation based on GRCh38? here, I read this post about this issue, however, it used genotypes.bcf file of GRCh37 (I couldn't find it for GRCh38), and also as this file is large, it takes almost long time to download and process. I guess this information may be generated before and stored in a databases.

Your suggestions and comments would be highly appreciated.

Answer 1

[Ram]

You'll need to combine a liftover operation on a 1000g VCF file (unless an hg38 version is already available) with a bcftools annotate operation. The annotate operation can copy over attributes from a reference VCF file to a target VCF file based on matching chrom, pos, ref and alt, assuming both VCFs are normalized.

The -c option lets you rename attributes while copying them over, so you can ensure names like AC don't clash/overwrite.