Closed rmpb94 closed 1 year ago
After some further investigation, I think I have been able to work around this issue.
Instead of using .vcf files, I have make .bed, .bim, and .fam files. However, the group file identifiers now need to be in the format 1:12324:A:G
not chr1:12324:A:G
. Within the step 2 command the --chrom
flag also needs to be specified as--chrom=chr1
The documentation doesn't make this very clear. It might be worth adding more explicit detail about the file specifications for the different file inputs.
Hi there. I'm seeing this under similar conditions. All error entries seem to refer the final variants in the affected groups (counter starts with zero). Output also mentions "Reach the end of the vcf file" in the preceding line of output.
Best I can tell is it's an error tripping up the VCF iterator used by the VcfClass::getOneMarker
function. Switching formats away from VCF seems like the most straightforward workaround.
Hi,
I'm currently trying to run SAIGE-GENE+ for a set based test, but keep coming across this error:
ERROR: Reading 24th marker failed
I am using vcf input, and the group file is ordered by chromosome position. Any idea what could be causing this error?