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vgteam / haplotype-aware-mapping-paper

Scripts for the haplotype-aware mapping paper project
MIT License
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BWA reads seem to be all wrong for BRCA1 #9

Closed adamnovak closed 6 years ago

adamnovak commented 6 years ago

I noticed that my test data from my last BRCA1 run has BWA mismapping 100% of the reads. I suspect this is related to BRCA1 having an offset (i.e. it doesn't start at cheomosome position 0) and the offset not being properly applied for BWA. I think mapeval needs a FASTA for just the region, which is the only way to get BWA in the same space as vg.

adamnovak commented 6 years ago

I've fixed this by passing region-specific FASTAs for BWA.