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Published 20 hours ago • verified publisher icon Illumina

Skipping low coverage genes

Open MichelledeGroot opened this issue 5 years ago • 2 comments

Hi,

I noticed that genes with a coverage below 10 are skipped in the calling. However, when I used your other tool GraphAlignmentViewer, I noticed that these images sometimes show a correct repeat size. Thats why I wanted to ask whether it is possible to lower the threshold of 10 since some images show a proper repeat size while they are skipped by ExpansionHunter.

MichelledeGroot avatar Dec 16 '19 07:12 MichelledeGroot

Yes, it makes sense that EH sometimes can correctly genotype repeats at low depths. We could consider reporting our best-guess genotype even when the depth is very low while setting the low-depth genotype filter. How urgently do you need this feature?

egor-dolzhenko avatar Dec 16 '19 15:12 egor-dolzhenko

It would be great if this feature could be added. It would be nice if it could be added within a month, but if it is not possible I could still use it later.

MichelledeGroot avatar Dec 16 '19 15:12 MichelledeGroot