Merge WGS and genotype data
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2.1 years ago
GK1610 ▴ 90

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 • 836 views
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1
Entering edit mode
2.1 years ago
Shab86 ▴ 280

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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