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.

Identify Compound Heterozygotes Using Select Variants

sboylesboyle Bay Area, CAMember

Hello Team,

Is there a best practice for finding compound heterozygotes using GATK? I can easily find recessive pattern variants using the SelectVariants tool, however, I have not been able to find a way to select compound hets. I am sure the Broad has a straightforward way. Is it somehow integrated into the GATK tool set?

I have considered using something like Gemini, but I would prefer to keep tools use to fewer product lines whenever possible.

Thanks for your help!


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Sean,

    Sorry to answer you so late. We have a little internal debate going on here about exactly what is meant by a compound het (it seems to mean different things to different people): are you thinking of two het sites side by side (which would be a phasing issue), or cases where you have both alleles mutated, so if REF is A, you're T/G?

  • sboylesboyle Bay Area, CAMember

    Hello Geraldine,

    In my case I'm interested in identifying when the gene copy from a mother contains damaging mutation A and the gene copy from the parent contains damaging mutation B. The parents in this case would be heterozygous for their own mutations and could be haplosufficient. The affected child however, would have two damaging copies and disease state. These mutations could either be at the same site (Such as in your second case) or what I believe you are referring to in your first case. I think phasing would be good here, but ultimately if you can pair up Damaging mutation A in only one parent and child and damaging mutation B in only one parent and child that would be sufficient to make the call. Some tools such as the ingenuity suite claim to be able to do this, however I would much prefer to stay with your suite. I was hoping that select variants could be used for this type of (If one from parent A and Child and other from parent B and child then output) situation.

    Thank you for your suggestions!

Sign In or Register to comment.