How to check and extract if a SNP is heterozygous or homozygous in a vcf file from the SNP ID
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4.5 years ago
akang ▴ 90

I have a vcf file and a list of SNP ids. I checked if SNPs are heterozygous/homozygous in my samples.

vcftools --vcf my vcf file.vcf --snp snp1 --extract-FORMAT-info GT | grep "0/1"

Now, I want to extract the sample ids that are either 0/1 or 1/1 and also i want to run an odds ratio test? Is there a way to do that in vcf tools?

VCF SNP • 3.5k views
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What is the format you need the data in ?

If you do not want to write a simple pysam script, you could do something like:

First clean the VCF such that you will end up with only het SNPs.

vcf-subset --exclude-ref --type SNPs in.vcf.gz > out.vcf

Then you could use the vcftools and no need to grep.

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To grep multiple patterns you can use the following command:

egrep "0/1|1/1"
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