I am running this command line in bedtools 2.27.1
bedtools coverage -nonamecheck -d -sorted -a file.bed -b file.bam > file.cov
and I get this error
ERROR: Database file file.bam contains chromosome chrM, but the query file does not. Please rerun with the -g option for a genome file. See documentation for details.
I don't have access to the genome file and I guess nonamecheck is not working,
Thanks a lot