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 https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

haplotypecaller indel format

dcittarodcittaro Member
edited September 2012 in Ask the GATK team

Hi there,
I've done with a run of HaplotypeCaller on my samples. I'm now analysing everything with snpEff, although I'm doing this "outside" GATK. I had to stop the analysis because a huge number of errors, all dealing with indels, such as:

Error while processing VCF entry (line 580649) :
    chr21   26718345    .   TAATCCTGAGTTTAA TATCCTAAATGTTTAC    943.26  […]
java.lang.RuntimeException: Insertion '-A+AT' does not start with '+'. This should never happen!
    chr21   35260360    .   CATAACAGTTCAT   AGAGACAGAG  425.22  […]
java.lang.RuntimeException: Deletion '+G-TTC' does not start with '-'. This should never happen!

Of course, this is a snpEff error, nevertheless the Indel format looks quite different from what I've ever seen. Consider the first line above: shouldn't it be like

chr21   26718345    .   AT  T   943.26  […]

(I can't resolve the second right now).
Any hint is appreciated at this point. I'm writing to snpEff developer for the same reason...

Post edited by Geraldine_VdAuwera on

Best Answer

  • ebanksebanks Broad InstituteMember, Broadie, Dev
    Accepted Answer

    Hi there,

    The first set of alleles does not reduce to AT/T. It's actually a much more complex substitution (you'll see if you look closely). The Haplotype Caller is doing the right thing here and this error lies solely in the snpEff code, so unfortunately there's nothing we can do to help you here.

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev
    Accepted Answer

    Hi there,

    The first set of alleles does not reduce to AT/T. It's actually a much more complex substitution (you'll see if you look closely). The Haplotype Caller is doing the right thing here and this error lies solely in the snpEff code, so unfortunately there's nothing we can do to help you here.

  • Thanks. I had the answer from the developer, he confirmed that SnpEff cannot handle mixed events.
    Well, at least you know that snpEff cannot handle (right now) those events, you may want to add some warning in the pages in which you suggest to use snpEff to predict variant effect.
    d

Sign In or Register to comment.