Open dym22 opened 2 months ago
It's possible this is related to your sumstats being in hg38, while 1KG is in hg19. The liftover step is imperfect and can result in losing certain SNPs: https://github.com/RajLabMSSM/echoLD/issues/11
Will look into whether there's a way to make the liftover more robust (if that is indeed the problem), or at very least provide the user with a more informative error.
I had not considered that but pretty easy fix--just ran MungeSumstats::liftover to get them in 19, adjusted everything else accordingly, and it ran without incident.
I'm going to try to get the in-sample LD version running when I have a little more time, but very relieved to at least have something to work with. Thank you so much for your help!
1. Bug description
When running finemap_loci on my 11 topSNPs, it proceeds successfully with 4 of them but fails for the other 7. The error (when it occurs) appears to happen during Step 2: Extract Linkage Disequilibrium. Specifically, for 7 of the loci, the console outputs "invalid 'path' argument" right after attempting to query the VCF tabix file.
2. Reproducible example
Note: the error also occurs when not using the forcenew* arguments. I am just including them so that it will reproduce the error as if running from scratch.
Console output
When running correctly:
When running incorrectly:
Data
3. Session info