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2.2 years ago
mmghaffar29
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0
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?
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.
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.