FastQTL fails to get genotype region
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5.1 years ago
Phoenix Mu ▴ 100

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 • 1.8k views
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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.

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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.

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