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COmbining gvcf files combing from TVC v.5.0.2

idaiosidaios imbb-forth heraklionMember

Dear GATK team,
I apologize if this is not the right place to ask, but I'm kind of desparate to find a solution to this...
so, I have installed the standalone version of TVC to get variants from Ion-Torrent bam files. TVC 5.0.2 can produce gVCFs. Thus, I was hoping that GATK will be able to combine them in a single VCF containing all samples and appropriate for population genetics analysis. Unfortunately, GATK crashes:

ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: java.lang.Integer cannot be cast to java.lang.Double

I guess this is happening because the genome.VCF I have is produced with TVC and not GATK. Is that right?

Do you have a solution to this? Are there tools that could combine gvcf files produced by TVC?

thanks a lot in advance

pavlos

Best Answers

  • SheilaSheila Broad Institute admin
    Accepted Answer

    @idaios
    Hi Pavlos,

    Yes, I suspect the program is crashing because the input is not formatted properly. Can you tell me the exact command your ran? Also, can you try running ValidateVariants on your input GVCFs?

    Thanks,
    Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    I'm afraid our official recommendation is "just don't use IonTorrent for sequencing" because it limits your options so much. You can try asking on SeqAnswers or BioStars; I'm not convinced you'll find a good solution but if you do please report it here to help others who might be in the same boat.

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin
    Accepted Answer

    @idaios
    Hi Pavlos,

    Yes, I suspect the program is crashing because the input is not formatted properly. Can you tell me the exact command your ran? Also, can you try running ValidateVariants on your input GVCFs?

    Thanks,
    Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The problem here is that these tools can only be run on GATK-produced GVCFS. There is currently no other software package that produces compatible GVCF files, that I know of. You simply cannot plug TVC output into the GATK joint calling workflow. There's no way to make it work.

  • idaiosidaios imbb-forth heraklionMember

    Hi Sheila and Geraldine,

    Thanks a lot for the answers.
    Sheila I'll report soon the command line I ran.

    Are you aware of any pipeline to proceed with data produced by an IonTorrent and eventually generate a multi-sample VCF?

    People from the IonTorrent community recommend using TVC. But as far as I know TVC cannot produce multisample vcfs. So I have to use external programs. GATK is not an option because gVCFs have to be produced by GATK. Perhaps bcftools ?

    pavlos

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    I'm afraid our official recommendation is "just don't use IonTorrent for sequencing" because it limits your options so much. You can try asking on SeqAnswers or BioStars; I'm not convinced you'll find a good solution but if you do please report it here to help others who might be in the same boat.

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