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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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Minor bug in target variants for GRch37 #17

Closed benz888-tech closed 2 years ago

benz888-tech commented 2 years ago

Hello @xiao-chen-xc,

I was running your program with GRch37 data and found a minor bug. I think you put the wrong position in the variant_name from file Cyrius/data/CYP2D6_target_variant_37.txt. For example, variant_name : g.42126611C>G where the real position should be 42522613. I also found the same issue in Cyrius/data/CYP2D6_target_variant_19.txt.

Thanks !

Best regards Benz

xiao-chen-xc commented 2 years ago

Hi Benz,

The variant name is based on the coordinate of the variant on HG38. This way we refer to a variant consistently regardless of the reference genome. It wouldn't affect the star allele calling because the star alleles are defined by variants named in this way.

Thanks, Xiao

benz888-tech commented 2 years ago

Ok, thanks for clarifying the issue. I will close this now.