I am using FastQTL (http://fastqtl.sourceforge.net/) for eQTL mapping in our genotyping (~20K SNPs) & RNA-Seq data. It basically uses a VCF file for the genotypes and a BED file for gene expression levels.
For genome-wide analysis it works very well so far; but I am missing information for some regions when it gives errors as it uses the GSL for maximum likelihood estimations during the permutation step. The error is as below:
''gsl: beta.c:44: ERROR: domain error. Default GSL error handler invoked. Aborted''
As I said, it doesn't occur frequently and for all the genetic regions. I checked the values in VCF and BED files many times, and they all seem OK. I analyze the genome in chunks, and if this error occurs in one of the chunks, I lose all the information in that chunk.
Since it says ''beta'', I think it might be about the beta functions, but I couldn't find more information to fix the problem. Any suggestions on this error?