I'm distributing variant calling across a number of cluster nodes. For each task, I specify the entire chromosome in a .bed file and provide it with the --callRegions option, i.e. a usual bed file looks like
1 0 248387328
It turns out that for such a task only the variants in the first Genome Segment (the first 12Mbp in the chromosome) are called. So, I found a workaround by commenting the following lines in share/strelka-2.9.10-1/lib/python/strelkaSharedWorkflow.py:
#if self.params.callRegionsBed is not None :#segCmd.extend(['--call-regions-bed', self.params.callRegionsBed])
This excludes the --call-regions-bed parameter when executing strelka2 on each genome segment. It seems that --region parameter is somehow incompatible with --call-regions-bed when the latter supplies a large region.
I'm distributing variant calling across a number of cluster nodes. For each task, I specify the entire chromosome in a .bed file and provide it with the
--callRegionsoption, i.e. a usual bed file looks like1 0 248387328It turns out that for such a task only the variants in the first Genome Segment (the first 12Mbp in the chromosome) are called. So, I found a workaround by commenting the following lines in
share/strelka-2.9.10-1/lib/python/strelkaSharedWorkflow.py:#if self.params.callRegionsBed is not None :#segCmd.extend(['--call-regions-bed', self.params.callRegionsBed])This excludes the
--call-regions-bedparameter when executing strelka2 on each genome segment. It seems that--regionparameter is somehow incompatible with--call-regions-bedwhen the latter supplies a large region.