Report AF independent of base quality filters

CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data

http://csb5.github.io/lofreq/

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Report AF independent of base quality filters #126

Open Paprikant opened 2 years ago

Paprikant commented 2 years ago

This PR fixes #80

The alternate allele depth after applying the base quality filter gets reported as a new info field HQA (name up for discussion). This way no information is lost compared to the previous version where HQA could be calculated as AF * DP

bgruening commented 2 years ago

@Paprikant great work! Thanks a lot for working on this. It's an important bug fix for us! Without this fix, it makes our COVID workflow more complicated than it needs to be.

Thanks!