Find common SNPs in multiple VCF files

Question

I have 3 VCF files.
A1.vcf
A2.vcf
A3.vcf

I want to get the common SNPs that are present in all these three files. And output must be in vcf format.
output:
common_A.vcf

jared_mamrot · Answer

A potential solution is to compress and index the files using bgzip and tabix, then use bcftools isec to find SNPs common to all three files, e.g.
for files in A1.vcf A2.vcf A3.vcf
  do
  bgzip "$files"
  tabix "$files"
done

bcftools isec -n=3 -c all -o all_common_SNPs.vcf A1.vcf.gz A2.vcf.gz A3.vcf.gz
```

Find common SNPs in multiple VCF files

One Answer

Add your own answers!

Ask a Question