basic question: number of callable bases

[gmd]

Can anyone help about "how we can find number of callable bases with a defined read depth from the bam file?" For example "the number of callable bases with read depth of 4"? I found GATK's callable loci tool but it seems this tool can just give the number of bases with a defined MAPQ. I also need a subset bam file which only have the callable bases with defined depth parameter in addition to the number of these bases. Thank you

[aeonsim]

Use the GATK Callable Loci tool with the mindepth & maxdepth options set to what you want and get it to output the bed file, read the Docs for details.

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_CallableLoci.html

Then filter the Bed file to select only the windows that meet your criteria Callable, Low_coverage, High_coverage etc and use bedtools to create an intersect BAM file from the original BAM & your filtered BED file.