Creating a set of rare variants shared by a child and a parents with VCF and Tabix

Question

[solene.conrad]

Hello,

I have two single WES from a child and his father. I would like to create a set a of rare variants inherited from the father. Afterwards, my goal is to compare if these rare variants still be found in a WES where I have pooled 2 fathers, to tests the sensibility of pooling.

I have been told that I could use Tabix but I don't know where to find the information on allele frequency in general population from GnomAD, to see what variants are rares? I could work on FastQ, cram and VCF formats.

Thank you!

Solène

Answer 1

[Nicolas Rosewick]

Some hints :

First filter only variants with a gnomAD AF under a certain threshold to be considered as rare ( < 1% ; < 0.1% , up to you) in the father and son vcf. To do that you could first annotate your VCFs using VEP (https://www.ensembl.org/info/docs/tools/vep/index.html) and then filter with filter_vep or bcftools

Then intersect father and son vcf using bcftools isec -n +2 father_rare.vcf son_rare.vcf