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Is it possible to do bedtools multicov across the entire genome?

Hi,

I would like to find the depth for each position in HG38 for my bams. I can do this for individual genes, but is it possible across the entire HG38?

Thanks,
Amy

bedtools
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updated by Ram Ram • written by hello_bioinf • hello_bioinf

2 answers

Simply use then bedtools genomecov with -d parameter : https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html

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written by Nicolas Rosewick Nicolas Rosewick

mosdepth (LINK) is an excellent/fast alternative.

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written by GenoMax GenoMax

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