Dealing with loci with no SNP

[ggittu]

Hi Huwenbo-

@shihuwenbo @huwenboshi I am trying to work this out for the step2, but I am getting error ,

[INFO] Loaded results for 1703 loci from step 1
[INFO] Using 1066727 SNPs with average sample size 8965.0
[INFO] Re-inflate the summary statistics with lambda_gc: 1
[ERROR] Rank of A less than the number of loci. There might be loci with no SNP.

From what is given in the FAQS, I made sure the sumstats file dont have any NA in the SNP column. What can I do to make this run ? Which SNP's from where should be removed? Is the --drop-missing-loci function implemented yet ?

Thanks Huwenbo

[meghatron21]

Hi. I wanted to follow up on this also. I am getting an error of Rank of A less than number of loci. Should I just use a different partiion function?

[Rick-Chen-PKU]

Getting the same error! Any advice to handle it?

[Rick-Chen-PKU]

I may have found the problem, there is little SNPs in a region on chr1:178944309-178954470 (see below). If use sumstat.gz data from LDSC to run the code, it may pop out an error!
The error will cause subsequent errors [ERROR] Rank of A less than the number of loci. There might be loci with no SNP.

[huwenboshi]

Hi, in this case, you will need to remove the region in the bed file, and rerun the analysis.