How to fill in missing fields on a VCF to convert into a genotype matrix?

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7.5 years ago

jespinoz ▴ 20

My VCF file looks like the screenshot below and I believe it is missing the necessary fields to convert it into a genotype matrix that I can actually use. It's 14GB and contains 88 samples.

How can I fill the missing fields (e.g. GT) and convert it into a genotype matrix with exact commands?

I've found references for similar questions that are one sentence answers with a link to a tool but many issues aren't addressed and I have yet to find a good tutorial on how to fill in missing fields on a VCF file and convert it to genotype/SNPs matrix.

Thank you : )

enter image description here

vcf genotype matrix bcf snps • 2.5k views

ADD COMMENT • link 7.5 years ago by jespinoz ▴ 20

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My first guess: those are probably missing because they weren't genotyped.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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I used samtools mpileup. How can I genotype them? I have all of the bam files still.

ADD REPLY • link 7.5 years ago by jespinoz ▴ 20

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You could check for one of the missing samples if that position is covered in your bam file.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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