Only the first Genome Segment called when putting entire chromosome in .bed file

[sergeyvilov]

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.