I have a my_vcf file containing genotypes of 600 individuals. These individuals are from European descent.
I want to use AF from 1000 genomes phase 3 project of European population.
I have subsetted 100 genomes phase3 vcf file for European population using following command.
vcf-subset -c EUR.samples.list ALL.chr13.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz | fill-an-ac | bgzip -c > EUR.chr13.phase1.vcf.gz
I want to add these Allele frequencies from here to my original my_vcf file.
How do I do this?