Extract samples from a VCF file that contain marker

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10 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 • 692 views

ADD COMMENT • link updated 10 months ago by WouterDeCoster 47k • written 10 months ago by Cèlia • 0

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Entering edit mode

contain specific SNPs that I have in a list

explain/describe

ADD REPLY • link 10 months ago by Pierre Lindenbaum 161k

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Possibly you mean Use bcftools to find carriers of variants

ADD REPLY • link 10 months ago by WouterDeCoster 47k

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