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!
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!