The current GATK version is 3.8-0
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!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
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.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Filtering Variants using the Format Column + JEXL Oddities

ericco92ericco92 Cambridge, UKMember

Hi Team,
I have a VCF which I'd like to filter by variant frequency. The problem is, my frequencies are percentages rather than decimals. Is there a workaround in JEXL which allows it to parse the '%' operator as a percentage (or ignore it entirely) rather than considering the field a string upon seeing the modulo operator?
The VCF also has two columns in the format column (a normal and a tumor). Is it possible to drill down into these using just the genotypeFilterExpression/genotypeFilterName flags or must do something else?

Eric T Dawson

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Eric,

    I'm not aware of any such workaround. At the risk of sounding naive, why not just convert your percentages to decimals? As workarounds go that's pretty trivial.

    Regarding the genotypeFilterExpression/genotypeFilterName, it depends what you want to do, but sure, you can filter on those too. We don't currently provide much guidance to doing so, however, so you'll need to experiment on your own, or appeal to others in the community for help...

  • ericco92ericco92 Cambridge, UKMember

    Hey Geraldine,

    I considered converting to decimals but figured I'd ask if there was a workaround first. I've got about 9000 files to work with and didn't want to risk breaking things. Guess I'll have to trust my sed skills after all.

    I'll play around with it and hope for the best. Thanks for the help!!

Sign In or Register to comment.