emit-ref-confidence error

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Camila Martínez Avila

• February 08, 2022 00:44

REQUIRED for all errors and issues:
a) GATK version used: v4.2.5.0
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.

Hello.

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.

Thanks.

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  Genevieve Brandt (she/her)

  • February 08, 2022 15:32

  Hi Camila Martínez Avila,

  Thanks for writing in! The command you mentioned is useful for viewing the read groups in your bam file. This makes sure that you have read groups in your file and also tells you the sample name(s) in your file.

  If there is nothing output from the command, you probably do not have read groups in your bam file. Check out our article on read groups and another article detailing how to add them to your bam file.

  Let me know if this solves your issue or if you have further questions.

  Best,

  Genevieve

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  Camila Martínez Avila

  • February 17, 2022 03:46

  Thanks a lot!
  I'm adding the information to my samples and I haven't had problems with the AddOrReplaceReadGroups function. I'm going to try running HaplotypeCaller on this fixed files and hope not to get any error.

  Again, than you very much.

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  Genevieve Brandt (she/her)

  • February 17, 2022 16:15

  Great! Let me know if the error comes up and I can help if so.

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