SAIGE GWAS - Single variant association tests cannot work
When I use the bgen file as the input file, as shown in Figure 1, the tasks fail as shown in Figure 2 （log）whether I run them individually or set them up as Batch Jobs. I would like to know how to resolve this issue.
Thank you
Comments
1 comment
Hi Shangyou,
There is a known issue where the GEL bgi files you are using can cause an issue with REGENIE jobs - I'm not sure if this will affect SAIGE as well, but can you try regenerating the bgi files using the instructions found here: https://community.ukbiobank.ac.uk/hc/en-gb/community/posts/17179207789853-How-to-resolve-REGENIE-errors-with-GEL-and-TOPmed-BGEN-indices
If this doesn't resolve the issue, can you give a bit more detail about how you generated the intermediate SAIGE files?
Thanks,
Daisy
Please sign in to leave a comment.