How to fill in missing fields on a VCF to convert into a genotype matrix?
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 : )
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jespinoz •
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My first guess: those are probably missing because they weren't genotyped.
I used samtools mpileup. How can I genotype them? I have all of the bam files still.
You could check for one of the missing samples if that position is covered in your bam file.