Question: Using Bedtools coverage to find BAM coverage?
0
gravatar for vctrm67
13 months ago by
vctrm6720
vctrm6720 wrote:

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?

bedtools • 356 views
ADD COMMENTlink modified 11 months ago by hahn5Thomas0 • written 13 months ago by vctrm6720
0
gravatar for Kevin Blighe
13 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

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

ADD COMMENTlink written 13 months ago by Kevin Blighe67k
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