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HKU-BAL / ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling
BSD 3-Clause "New" or "Revised" License
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Get a large number of variants from ClairS-TO #7

Closed ywzhang071394 closed 2 months ago

ywzhang071394 commented 3 months ago

Hi, I am using Clairs-TO to call somatic small variant from PacBio Revio tumor data. As a result, ClairS-TO detected ~28000 variants, which is much larger than I expected. I am not sure whether there are many false positive and thus post this issue to enquire if it's normal condition when using ClairS-TO.

Thanks!

aquaskyline commented 3 months ago

Quite a number of variants in your 28k calls are germline, do you have any PoNs for filtering the calls?

ywzhang071394 commented 2 months ago

We used the default PoNs, which is embedded in the ClairS-TO package.

aquaskyline commented 2 months ago

You might want to find or construct a PoN that is specific to your cancer type or population to further reduce the number of variants.