SAIGE-GENE: Is it possible to analyse chrY?
Hey,
I'm trying to run SAIGE-GENE for Y-chromosomal variants in an all-male sample. However, I receive this error:
ERROR: 24:6866079:C:T has minimum ploidy = 1 (not 2)This makes sense of course, but I can't see any parameters or anything I could specify for SAIGE to skip these checks.
The analysis of chrY in SAIGE-GENE must be possible however, as e.g. Karczewski et al. have done it.
Does anyone have any ideas or advice how to get this to work?
Comments
1 comment
I suggest you ask this question on the ukb genetics jiscmail group.
See https://www.ukbiobank.ac.uk/enable-your-research/manage-your-project which says
“Several JISCMail mailing lists have been established to facilitate community support of researchers utilising specific UK Biobank datasets. These mailing lists are set up and managed by members of the research community to enable discussion and knowledge exchange regarding UK Biobank datasets, and are an excellent resource.”
direct link https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ukb-genetics&t=&X=A68CABDA7E8320211B
I think you would need to create a login for it.
Alternatively, you could try contacting the corresponding author on the Karczewski paper.
Please sign in to leave a comment.