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Merge WGS and genotype data

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?

snp
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updated by Biostar Biostar • written by GK1610 GK1610

1 answer

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!

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written by Shab86 Shab86

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