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.

Homopolymeric error sites

How does GATK2 handle the variants called at homopolymeric regions in the genome? Is this feature enabled and used during the variant calling (with UG/HC) or should we do it separately with VariantFilteration. Is there any specific parameter to control this?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Raj,
    Currently they are not handled specifically. There is a VariantAnnotator annotation called HRun that looks at homopolymers, but unfortunately it doesn't work very well so we no longer use it in our Best Practices.

  • vsravivsravi Member

    Hi Geraldine, Has there been any update to calling variants near homopolymer runs? From my experience, the most common case of false-positive indel calls from GATK UG are near homopolymer sites. It would be nice to have the option to apply stricter criteria for calling indels near homopolymer sites.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Ravi,

    Not internally in the UG, and unfortunately we haven't been able to devote any resources to fixing the HRun annotation. However, the HaplotypeCaller is much better at dealing with this problem. So unless you absolutely have to use the UG (because of ploidy or cohort size) you should try using the HaplotypeCaller. If you do, we'd be interested in hearing back from you on whether you see an improvement in those calls.

Sign In or Register to comment.