Report AF independent of base quality filters #126
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added 2 commits
February 28, 2022 17:16
… bases a given snp call is based on
wm75
referenced
this pull request
in galaxyproject/iwc
Mar 15, 2022
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@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! |
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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