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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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DEV-3740: Adjust for germline deletions heterozygous in tumor #507

Closed DFKoetsier closed 5 months ago

DFKoetsier commented 5 months ago

Add "Potentially pathogenic heterozygous germline deletions" section to PDF. Add "germlineHeterozygousDeletions" and "reportableGermlineHeterozygousDeletions" to JSON. Extend derivation of reportable germline deletions from reportable germline disruptions to deletions heterozygous in the tumor. Convert deletions heterozygous in tumor to somatic LOH events when converting germline events to somatic events. Make some improvements to detection of somatic LOH regions based on germline deletions. Change title of somatic LOH section on PDF.

DFKoetsier commented 5 months ago

I have incorporated the feedback, including the suggestion to only create at most one PurpleLossOfHeterozygosity and PurpleGainLoss object per gene in PurpleInterpreter. I have also improved the merging of germline and somatic LOH in GermlineConversion, and I have added similar merging for germline and somatic losses.