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HC in gVCF mode gives error "Can only be used in single sample mode" when passed 4 bams for sample

daniel_adkinsdaniel_adkins Member Posts: 14

i have been using HaplotypeCaller in gVCF mode on a cohort of 830 samples spread over 2450 bams. the number of bams per sample varies from 1-4. for samples with <=3 bams, the routine works perfectly. but for samples with 4 bams, the jobs always crash and I receive the error:

ERROR MESSAGE: Invalid command line: Argument emitRefConfidence has a bad value: Can only be used in single sample mode currently

is this a bug? are there any options i can use to avoid this error. i suppose it is possible that there is an issue with my bams, but it seems odd that the error occurs systematically with 4 bam samples and never for samples with 3 or fewer bams.

thanks for any help!

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Answers

  • daniel_adkinsdaniel_adkins Member Posts: 14

    you are right, geraldine. was a read group SM tag issue.

  • d_t_nguyend_t_nguyen Member Posts: 2

    Hi Geraldine,
    I have the same error with Daniel: "ERROR MESSAGE: Invalid command line: Argument emitRefConfidence has a bad value: Can only be used in single sample mode currently" when I run HaplotypeCaller with ERC mode for 3 samples of 1000 Genomes Project. Could you help me to figure it out?

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,704 admin

    Hi @d_t_nguyen,

    Sorry for the late reply. I'm not sure what there is to figure out; the error message states fairly clearly that HaplotypeCaller can only be run on one sample at a time in ERC mode. That means you can't run it on three samples together...

    Geraldine Van der Auwera, PhD

  • d_t_nguyend_t_nguyen Member Posts: 2
    edited May 2014
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