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seppinho / haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
https://haplogrep.i-med.ac.at/
MIT License
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Issues with processing indels in VCF #40

Open shadrinams opened 3 years ago

shadrinams commented 3 years ago

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!

seppinho commented 3 years ago

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