A method to count genotype ALT amounts for a vcf file with 3 samples?

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3.7 years ago

kadamek49 • 0

Hello,

I have a vcf file with 3 different samples that are compared to the reference genome. I am looking for a way to count the ALT genotypes that appear for each sample. But I would like to take this a step further by using some code to look into the accumulating variants. Thus, I would like to view counts of ALTs genotypes appearing in sample 1 + 2, and sample 1+2+3. I am currently looking into methods using the following: vcftools, bcftools, vcfR, java, and perl. Any help would be greatly appreciated! Thank you.

gene vcf genome sequence • 777 views

ADD COMMENT • link 3.7 years ago by kadamek49 • 0

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bcftools should do this, you can select all hom-ref/het/hom-alt loci in a subset of samples. You might need to run the query a few times, but it should be straightforward.

ADD REPLY • link 3.7 years ago by Ram 43k

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