This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
HaplotypeCaller single sample mode error
I am trying to run GATK4 HaplotypeCaller on a bam file from a single individual on Ubuntu 18 with
gatk HaplotypeCaller -R Tse_SBAPGDGG_D.fa -I AHP2746_sorted_dedup.bam -ERC GVCF -O AHP2746.gvcf
But I get the error:
A USER ERROR has occurred: Argument --emit-ref-confidence 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.
Anyone know why this error is being thrown? The input bam file is not multi-sample, it is a bwa generated bam file then sorted and deduped by elprep. It is from a single individual.