bedtools version 2.16.2 multicov used to compute the multiple sample coverage given a feature file(gtf bed).
format: bedtools multicov -bams alin1.bam aln2.bam .. -bed capturRegion.bed >out.coverage
official doc has mentioned that input bam files should be sorted and indexed, but it does not mention the details. suppose the bam file name is: sample1.bam, then the index file should be named: sample1.bam.bai(not sample1.bai) ,otherwise multicov will report an error: indexes not found.
I think it would be better to add an option which will allow the user to specify the bam index files or the suffix used for these index files.