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Genotypes in vcf files

Hi! I have a question my VCF files have weird genotypes in it like some with 0/2 or 0/3, some with 1/2, 1/9, 2/2, 2/1, 4/13, 6/6. Should I only keep 1/1 as homozygotes?

genotypes exome
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updated by jena • jena • written by mmghaffar29 • mmghaffar29

Please provide a snippet of a few lines from your file, and also give some more details on the source and contents of your VCF.

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written by liorglic liorglic

Hi and welcome. How many alternative alleles do you see in the ALT column at these positions? The encoding is as follows: 0=REF, 1=1st ALT, 2=2nd ALT and so on. So for example the genotype 0/3 means a heterozygous individual with one reference allele (REF) and one allele describer by the third entry in the ALT column.

Since there are only 4 possible bases, the other alleles are typically indels. You may wish to remove those (with packages like bcftools) or keep them, depending on the questions of your study.

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written by jena • jena

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