I am trying to use bedtools coverage to compute the depth at particular SNP sites that I list in a BED file. I am running this command:
bedtools coverage -a sample.bed -b sample.bam -mean > test
However, the output seems to list that the average coverage per site in the BED file is 0. I don't think this is true because I also ran GATK's DepthofCoverage, and it differs dramatically from what bedtools shows. Am I using bedtools incorrectly?