If I leave out the -sorted -g ref.dict options it works just fine.
The -b file is missing some chromosomes from the -a file. I cannot share the BED files as they are confidential, but I'll keep trying to find a small reproducible test case. Version 2.27.1
If I leave out the
-sorted -g ref.dict
options it works just fine.The
-b
file is missing some chromosomes from the-a
file. I cannot share the BED files as they are confidential, but I'll keep trying to find a small reproducible test case. Version 2.27.1