REQUIRED for all errors and issues:
a) GATK version used: v126.96.36.199
b) Exact command used: gatk HaplotypeCaller -R Pcaerulea_nuclear.fasta -I 070_nodups.bam -O 070.g.vcf.gz -ERC GVCF
c) Entire program log: 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.
It's my first time using GATK and this error came up. I've seen antoher post about this and you recommenden running this:
samtools view -H sample.bam | grep '@RG'
But nothing outputs. I've also tried with other files from the same project but the same happened. I would appreciate any help with this.
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