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HaplotypeCaller multi-sample error on single sample

I have 2 questions:

1. I am running HaplotypeCaller on a single whole-exome BAM file. However, I get this error message:

A USER ERROR has occurred: Argument --emitRefConfidence has a bad value: Can only be used in single sample mode currently. Use the sample_name argument to run on a single sample out of a multi-sample BAM file.
I believe this should be a single-sample BAM file, but I'm not sure how to check.

2. Are gVCFs outputted by parallelizing HaplotypeCaller mergable into a single gVCF for further analysis?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


    Can you please post the version of gatk you are using, the exact command and the entire error log.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Can you check the bam header and post here. Your bam file may include multiple sample names and a single read group instead of a single samplename and multiple readgroups. In that case you need to realign your reads to reference with proper samplename and readgroup identifiers.

    To check the header of your bam file run

    samtools view -H bamfile
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