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I have question about Genotype information in SVtyper output #123

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u1200538 opened this issue Jun 9, 2021 · 0 comments

u1200538 commented Jun 9, 2021 •

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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.

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?
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!

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