How to calculate genome coverage

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

genome next-gen-sequencing

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updated 4.2 years ago by Ram 4.5K • | written 11.4 years ago by chchl7 4

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.

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updated 4.2 years ago by Ram 4.5K • | written 11.4 years ago by Ashutosh Pandey 1.2K

Thank you very much! I'll try.

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written 11.4 years ago by chchl7 4

2 answers

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

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updated 4.2 years ago by Ram 4.5K • | written 11.4 years ago by awagner 3

Thank you, I will try.

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written 11.4 years ago by chchl7 4

Use Bedtools

There are tutorial all around

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written 11.4 years ago by Antonio R. Franco 519

Thank you very much!

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written 11.4 years ago by chchl7 4

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