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ding-lab / CharGer

Characterization of Germline variants
https://ding-lab.github.io/CharGer/
GNU General Public License v3.0
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Fix bug #19

Closed icebert closed 5 years ago

icebert commented 5 years ago

  1. minPathogenicScore could be equal.

  2. var.splitHGVSc doesn't consider strand information. When override = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts.

icebert commented 5 years ago

If override = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts. Because in splitHGVSc, it only replaced the ref and alt without considering the strand. There is no need to replace the ref and alt here.

https://github.com/AdamDS/BioMine/blob/d76b619c9b60c80e43bf29354f96547905e64cee/biomine/variant/mafvariant.py#L497-L499

icebert commented 5 years ago

For insertion and deletion, the start, stop, ref and alt were transformed in the readVCF:

https://github.com/ding-lab/CharGer/blob/b4a13b1456f3bbb26ab95e9f9151eb58756187a6/charger/charger.py#L257-L265

In the getMacClinVarTSV, the variants should be processed in the same way to match.

fernanda-rodrigues commented 5 years ago

Issues fixed in release v0.5.3