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Published 20 hours ago • verified publisher icon seppinho

Issues with processing indels in VCF

Open shadrinams opened this issue 3 years ago • 1 comments

Hello, I am using VCF files (created by Mutect) as input for haplogrep2 and I am having issues with processing indels, which are longer than 1-bp.

I had to change "285 GAA -> G" to two variants: "286 A -> * " and "287 A -> * " and only then haplogrep recognized the deletion. I still cannot make it to pass insertions. I tried to replace "1760 G->GT" to "1761 * -> T" but haplogrep complains about "​ * ". When I use "1760 G->GT", haplogrep2 recognize it as "1760G".

Is it expected behavior and how can I fix it? Thank you!

shadrinams avatar Mar 05 '21 18:03 shadrinams

Hi, Sorry for the late response. Can you provide an example so I can fix that.

seppinho avatar Aug 18 '21 09:08 seppinho