DepthOfCoverage intervals

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Andrea Franceschini

• December 01, 2020 12:35

I am using DepthOfCoverage on GATK 4.1.9.0 

The tool requires an --intervals parameter.

I wonder how should I set that parameter for whole genome wide studies.

Why that parameter suddently became mandatory ?

Thx a lot

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  Genevieve Brandt (she/her)

  • December 01, 2020 19:29

  Hi Andrea Franceschini, DepthofCoverage was introduced in GATK 4.1.6.0 and has had intervals as mandatory in all GATK4 releases. You can read more about the development here and the release notes here. We also have documentation on intervals, which can be found here.

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