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bioinfo-pf-curie / TMB

Tumor Mutational Burden
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`--filterLowQual` does not work #21

Open bounlu opened 10 months ago

bounlu commented 10 months ago

It works fine without the filter --filterLowQual. When I add this filter, no variant is selected and TMB is always 0. It seems there is a bug with the filtering.

nservant commented 7 months ago

Hi, Thanks for the comment. The --filterLowQual filter only keep PASS variants. Do you have a PASS flag in your VCF ?

bounlu commented 7 months ago

Yes I do and that's also my expectation but it somehow doesn't work.

bounlu commented 1 month ago

Here is the bug: https://github.com/bioinfo-pf-curie/TMB/blob/97ee724ac5860822ec59177e43456634067d652a/bin/pyTMB.py#L409-L413