Question: How to apply vcftools --diff to identify vcf-specific variants/records
gravatar for Shicheng Guo
5 days ago by
Shicheng Guo7.5k
Shicheng Guo7.5k wrote:

HI All,

Apply vcftools --diff, it is easy to find command/shared variants between two VCF files.

vcftools --vcf  A.vcf --diff B.vcf --diff-site

However, Is there any easy to identify A specific or B specific variants?

Here is what I noticed:

Parameters as interpreted:
        --vcf gnomad.exomes.r2.1.sites.chr21.rec.ExomeStop.vcf
        --diff gnomad.exomes.r2.1.sites.chr21.rec.ExomeStop.vcf.vat

After filtering, kept 0 out of 0 Individuals
First Header entry should be #CHROM: #OM
Outputting Discordance By Site...
Found 1696 sites common to both files.
Found 57 sites only in main file.
Found 0 sites only in second file.
After filtering, kept 1753 out of a possible 1753 Sites
Run Time = 0.00 seconds

I want to extract these 57 sites which only belong to main file (the first file)


Sorry. It looks I find the solution:

 awk '$3==1' out.diff.sites | wc -l
vcftools --diff-site --diff • 58 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by Shicheng Guo7.5k
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