Obtaining coverage of genome from Bam Files
Greetings friends,
I am attempting to obtain how much coverage my bam files have relative to my reference genome. I was wondering what kind of tools were available for this? I thought samtools would have some kind of function built in for this kind of task but I can't seem to find one. Any suggestions would be appreciated.
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Hello ggman!
Questions similar to yours can already be found at:
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I also added this answer to Tools To Calculate Average Coverage For A Bam File? :
A modern, very fast, solution for this would be mosdepth.
Of course the other answers are also valid.
samtools have
samtools depthandsamtools bedcov.bedtools has
bedtools coverage.Google has many suggestions:
Tools To Calculate Average Coverage For A Bam File?
Coverage per contig from a BAM file
Calculate Coverage From Bam File