Tagged with #callableloci
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A new tool has been released!

Check out the documentation at CallableLoci.

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Does the CallableLoci walker in GATK 3.3-0 generate 0-based or 1-based coordinates when invoking --format BED?

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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!