svtyper
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I have question about Genotype information in SVtyper output
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.
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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?
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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!