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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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I have question about Genotype information in SVtyper output #123

Open u1200538 opened 3 years ago

u1200538 commented 3 years ago

Hello,

I run the svtyper by using lumpy SV vcf file as a input. When I saw the genotyped sv file, it contained "./.", "0/0 genotype information.

image

  1. In case of "./." genotype, as you can see above image, Those line's had a "." values in GQ and SQ section. Is it a validate data?

  2. I think "0/0" genotype is not a suitable definitions of genetic variants category. Because, REF allele is same with ALT allele.

how do I interpret two kinds of the question that I wrote?

Thank you!