FastQTL fails to get genotype region
0
0
Entering edit mode
4.2 years ago
Phoenix Mu ▴ 60

I am using fastQTL to do QTL mapping and got the following error:

ERROR: Failed to get region chr1:0-111675033


I think the tool is not very well documented and just do not know how to slove the problem.

fastqtl • 1.5k views
0
Entering edit mode

What is the command-line you used to run FastQTL? Are you sure 111675033 bases falls within the length of chr1? Maybe region must be one-based indexed?

edit: it seems --region must be one-based:

The region of interest is specified with the standard chr:start-end format.

0
Entering edit mode

Thank you for your reply. I already figured it out that the error was because I have different chromosome names in VCF files and phenotype files. One has "1" whereas the other has "chr1". There is no error after I used bcftools to rename the chromosomes in VCF.