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awilfert / PSAP-pipeline

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Y Chromosome #13

Closed dconrad closed 7 years ago

dconrad commented 7 years ago

Y chromosome variants are not being properly assessed. There appear to be two weird things going on: 1) Y genes have been ommitted from the lookup tables (although we have generated null distributions for Y genes, so should be an easy fix) and 2) raw CADD scores appear to be missing for most Y-linked gene variants in ANNOVAR output. Its not clear at this moment if this is an ANNOVAR issue or a CADD issue. However, the PSAP pipeline currently on github is based on Phred-scaled CADD scores so we should be able to implement PSAP for Y variants very quickly.

dconrad commented 7 years ago

This has now been fixed. There are 22 genes on the Y with coverage in ExAC. Unfortunately, there are no Y-linked genes covered in gnomAD at the moment! I hope this doesn't become a trend.