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arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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Bedtools subtract misses whole chromosomes when -sorted -g ref.dict #142

Closed nh13 closed 5 years ago

nh13 commented 5 years ago

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

arq5x commented 5 years ago

Could you move this to the bedtools2 repo? Also, are the BED files in the same chrom order as the chroms in the -g file?