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Can CallableLoci functionality be expanded to add multiple coverage cutoffs

igcocoleigcocole Posts: 7Member
edited November 2012 in Ask the GATK team

Dear GATK team,

I have a question regarding adding the functionality to CallableLoci to allow multiple coverage cutoffs (similar to the -ct option in DepthOfCoverage) for LOW_COVERAGE. Basically for example COVERAGE_BELOW_10X, COVERAGE_BELOW_20X etc.

These multiple statistics are important for WGS interpretation, not just a single LOW_COVERAGE value.
At this point a separate DepthofCoverage instance has to be run (to do the same job twice) and takes much additional time. Instead of a single pass CallableLoci.

A simple patch to the CallableLoci code does the job, but it would be great if this can be implemented in the build as a simple command line option.

Thank you!

Post edited by Geraldine_VdAuwera on


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