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lgragert / srtr-impute-pubsaf2306

Extract HLA typing from SRTR and format data for 9-locus high resolution HLA imputation
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Update AAMM code to include only exon 2 position for Class II loci #13

Open lgragert opened 10 months ago

lgragert commented 10 months ago

Currently aa_mm_biopython_runmatch_genie_9loc.py prints out mature protein positions for Class II.

The ard_start_pos and ard_end_pos aren't actually the ARD - Grace updated these to be the mature protein coords, so rename these as mature_start_pos and mature_end_pos. Revert the coords back for ARD to older version of kidney-outcomes-sfvt to recover the correct ARD coords.

We might also want coords for just exon 2 and 3 because those should accurate for Class II. ARD is exon II only.