I know that I can create a subset of a bam file for a desired region using
samtools view -b UWNsub100k_int.bam chrXII:450000-470000 > UWNsub100k_ribos.bam
What I want to do, however, is create a .bam file that excludes these regions. Perhaps something similar to -v for grep. Is there a samtools command for this?
bedtools complementto generate the complement of chrXII:450000-470000