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Merge VCF files after Beagle : bad option for CombiVariants

TiphaineTiphaine Member
edited October 2012 in Ask the GATK team

Hi,

I don't understand error message from CombiVariants. I uses a command line from http://gatkforums.broadinstitute.org/discussion/43/interface-with-beagle-software#Merging_VCFs_broken_up_by_chromosome_into_a_single_genome-wide_file.
In documentation, you talk about this option : - variantMergeOptions UNION. But in your example, you give this option -type UNION.
But none of these options exists. I find only this option variantMergeOptions.

what is the good option and the value of this option to merge all vcf files from all chromosomes phased by beagle?

Thanks,
tiphaine

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Hi Tiphaine,

    Command line arguments change as we make progress with tool developments, so command lines given as examples in documentation articles are not always up to date. For the most accurate and up to date options list, please always see the technical documentation (aka GATKDocs) for each tool here:

    http://www.broadinstitute.org/gatk/gatkdocs/

    Note that these documents apply to the latest version of the GATK, so if you are using an older version, you'll need to use the argument list invoked with -h on the command line.

Answers

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

    Hi Tiphaine,

    Command line arguments change as we make progress with tool developments, so command lines given as examples in documentation articles are not always up to date. For the most accurate and up to date options list, please always see the technical documentation (aka GATKDocs) for each tool here:

    http://www.broadinstitute.org/gatk/gatkdocs/

    Note that these documents apply to the latest version of the GATK, so if you are using an older version, you'll need to use the argument list invoked with -h on the command line.

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