The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

#### ☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# Can CallableLoci functionality be expanded to add multiple coverage cutoffs

Member Posts: 7
edited November 2012

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
Tagged:

If you have a patch to make it a command line option, we're happy to look at it and consider including it in the build.

Geraldine Van der Auwera, PhD

• Member Posts: 37

Hi, is CallableLociWalker still in existence?, thanks.

Best way to find out is to look it up in the Technical Documentation... :-)

Geraldine Van der Auwera, PhD

• Member Posts: 37

Ah ha, thanks!
I must be being dense then as I can't get it to work. I'll look at the command line again and if I'm still having trouble, I'll post a message and appeal for help!, thanks.

• Member Posts: 37

Hi, realised my error, the page http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_CallableLoci.html suggests -T CallableLociWalker whereas it should be -T CallableLoci, thanks.