How to calculate genome coverage
2 answers
Use Bedtools
There are tutorial all around
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Antonio R. Franco
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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.
Thank you very much! I'll try.