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

Question

[amy__]

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

Answer 1

[Nicolas Rosewick]

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

[amy__]

Amazing, thank you so much!

BW, Amy

Answer 2

[GenoMax]

mosdepth (LINK) is an excellent/fast alternative.