How to calculate genome coverage

Question

[chchl7]

Just got genome re-sequencing data and want to know the percent of genome covered. Any cool idea? Thanks!

[Ashutosh Pandey]

You can use http://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics OR https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php

I would prefer CollectWgsMetrics for simple statistics as it is much faster than DepthOfCoverage.

[chchl7]

Thank you very much! I'll try.

Answer 1

[awagner]

You should check out bedtools genomecov. You can find a tutorial here.

[chchl7]

Thank you, I will try.

Answer 2

[Antonio R. Franco]

Use Bedtools

There are tutorial all around

[chchl7]

Thank you very much!