Extract samples from a VCF file that contain marker

0

Entering edit mode

17 months ago

Cèlia • 0

Hey!

I have a vcf file from which I want to extract the samples (genotypes) that contain specific SNPs that I have in a list. That is since I ran a GWAS and came up with significant SNPs that might explain my phenotype. I want to see if the SNPs are correlated and for that, I only want to keep the genotypes that contain such SNPS.

Is it possible to use bcftools for that?

Thank you in advance!

bcftools SNPs • 917 views

ADD COMMENT • link updated 17 months ago by WouterDeCoster 47k • written 17 months ago by Cèlia • 0

0

Entering edit mode

contain specific SNPs that I have in a list

explain/describe

ADD REPLY • link 17 months ago by Pierre Lindenbaum 164k

0

Entering edit mode

Possibly you mean Use bcftools to find carriers of variants

ADD REPLY • link 17 months ago by WouterDeCoster 47k

Login before adding your answer.

Similar Posts

Loading Similar Posts

Traffic: 1872 users visited in the last hour

Content Search
Users
Tags
Badges

Help About
FAQ

Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the

version 2.3.6