Improved functionality for X and Y

Open arq5x opened this issue 10 years ago • 3 comments

E.g., de novos on the X in males will be missed as we currently require a HET genotype.

Jul 01 '15 14:07 arq5x

A de novo in PIGA was missed on the X in a male because GATK called mom and dad HOM_REF yet male proband as HOM_ALT (when really HEM_ALT). We should make sure the de_novo tool uses special logic for this.

Sep 13 '16 15:09 arq5x

this was missed by x-linked-denovo?

Sep 13 '16 15:09 brentp

No, was missed by de_novo. I think we should try to just make de_novo run the logic in x-linked-denovo as it is just another chromosome on which to look for de novos. Most people won't think to run both separately.

Sep 13 '16 15:09 arq5x