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
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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.
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.
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