Hello,
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?
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written
by
vctrm67 •
1 answer
You may want to switch the BAM to be 'a' and use -abam, and also add the -d command line parameter. Please take a look through the documentation: https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html
Also check that your contig names are the same in both 'a' and 'b'.
Kevin
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