Merge WGS and genotype data

Question

[GK1610]

I have a genotype data vcf file of 100 individuals filtered for maf >.01 and then I take wgs file of another 50 individuals

and I intersect the sites that are common in both genotype and wgs data.

I merge the wgs and genotype data for these common sites using bcftools

This new merged vcf file has sites that have MAF of genotype file. How do I update the MAF in new merged vcf file?

Answer 1

[Shab86]

I would suggest you look at these biostars replies:

1. A: Merging vcf files (intersection and union)
2. A: How to use bcftools to calculate AF INFO field from AC and AN in VCF?

Hope this helps!