emit-ref-confidence error
Answered
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: gatk4-4.1.4.1
b) Exact command used: gatk HaplotypeCaller -I alignment_bwa/Nicolas-M2S2.sort.rg.md.filt.bam -R ./index/H37Rv.3.fa -ERC "GVCF" -O GATK/gvcf/Nicolas-M2S2_GATK.g.vcf 2> GATK/gvcf/Nicolas-M2S2_GATK_HC.log
c) Entire error log: 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.
If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?
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Hi Florence Morel,
Does your BAM file contain multiple samples? HaplotypeCaller is meant to be run on one sample. You can use the --sample-name argument to select the sample from your BAM.
Hope this helps!
Genevieve
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Thank you Genevieve for your quick answer!
Where can I find the sample name and how should I write the command line with the --sample-name argument?
Could you provide me an example?
Thank you +++
And best wishes for the new year!
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Hi Florence,
I just noticed a possible issue in your command, you have -ERC "GVCF" while it should be written as just -ERC GVCF. Try that and see if it solves your issue.
More information at the HaplotypeCaller documentation page: https://gatk.broadinstitute.org/hc/en-us/articles/360050814612-HaplotypeCaller#--emit-ref-confidence
Example Command:
gatk --java-options "-Xmx4g" HaplotypeCaller \ -R Homo_sapiens_assembly38.fasta \ -I input.bam \ -O output.g.vcf.gz \ -ERC GVCF
Happy New Year!
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Hi Florence Morel,
Did you ever get an answer to this question: "Where can I find the sample name and how should I write the command line with the --sample-name argument?"
I am having the same issue.
Thanks,
Julie
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Hi Julianne Radford,
I can give you an example for the sample name argument!
The sample names should be in your read groups, you can find more information at our documentation page here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
gatk --java-options "-Xmx4g" HaplotypeCaller \ -R Homo_sapiens_assembly38.fasta \ -I input.bam \ -O output.g.vcf.gz \ -ERC GVCF
--sample-name name_of_sampleHope this helps!
Genevieve
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Thank you so much for the feedback.
First question: do I have to include this bit in my HaplotypeCaller code? Because I haven't been as it returns an error when I try to use it.
--java-options "-Xmx4g"
Second, my bam file only contains one sample, but when I use the instructions from the Read Group page:
samtools view -H SRR5341585.bam | grep '@RG'
to find out the sample name, my shell returns the error:
E26: Hebrew cannot be used: Not enabled at compile time
However, I in my most recent effort, I used the --java-options "Xmx4g", and tried using the name of the BAM file which SHOULD be the sample name in the --sample-name name_of_sample argument, and now I am getting a new error:
A USER ERROR has occurred: 'HaplotypeCaller-R' is not a valid commandAnd I guess here the -R is referring to where I am putting in my reference file.
Any ideas? Thanks once again,
Julianne
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Hi Julianne Radford,
Go ahead and make a new post regarding these issues so we can look into solving them.
Thank you,
Genevieve
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Can I ask what exactly is needed in the --sample-name argument?
I'm struggling because my samples were split across lanes. I ran the alignments on those split samples, and sorted the individual alignments before using samtools to merge them into a sample_merged.bam file.
samtools merge -@ ${THREADS} ${SAMPLE}/${SAMPLE}_merged.bam ${SAMPLE}/*_sorted.bamNow I'm getting the same error message described above:
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.
In this case is --sample-name passed the SM information in the @RG? Currently my merged .bam files contains a read group for each sample that was merged. Will HaplotypeCaller only work on 1 of the samples in that merged file?
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Yes, if you are running HaplotypeCaller with -ERC GVCF, it will only run on one sample at a time. Our recommended joint calling pipeline involves running HaplotypeCaller on each sample individually, then consolidating the GVCFs with GenomicsDBImport or CombineGVCFs, and joint genotyping with GenotypeGVCFs.
Here an article regarding joint calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035890431-The-logic-of-joint-calling-for-germline-short-variants
And our joint calling pipeline for germline SNPs and Indels: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-
Hope this helps!
Genevieve
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Not sure what to do get past this error other than finding another tool somewhere else.
I don't have a @RG line in my bam or any mention of a "sample".
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Hi Marco Hoog, thanks for posting here! We can help out. You should be able to get past this issue if you add read groups to your samples, which are necessary for running GATK. There is more information about adding read groups at this troubleshooting document: Errors about read group (RG) information.
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Hi, I am having the same issue, I found that I needed to add the @RG read group information but I am trying and I have found that some of the documents provide incomplete information. For example, I went to this page which was recommended before - https://gatk.broadinstitute.org/hc/en-us/articles/360035532352, and I ran the code and I got an error: "ERROR: Option 'RGPU' is required.", which is not mentioned there.
I have processed just a few samples and I would like to know which information must be part of the @RG. I would like to start everything well from the beginning/mapping the reads, instead of having to fix this later.
I use bwa-mem, and one can add the read group information <<-R STR read group header line such as '@RG\tID:foo\tSM:bar' [null]>>.Thank you.
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Thanks for the feedback Juan Pablo Aguilar Cabezas! I'll submit a documentation request with our team to update that article with all the required read group fields.
There is a better description of the required fields in this article here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
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Genevieve Brandt (she/her) Do you know how to add it for the mapping step?
I am trying the AddOrReplaceReadGroups (Picard) but since there is no multi-threading option it for one sample it is taking almost 2 hours, the time it takes me to do the mapping-bam conversion and MarkDuplicate steps. -
Yes, you can add the read group fields in the order you can see in that read group doc I shared above! The command will be following the description from the bwa docs, '@RG\tID:foo\tSM:bar'. The '\t' inserts tabs and the different fields should replace ID and SM with the values for those fields.
@RG ID:H0164.2 PL:illumina PU:H0164ALXX140820.2 LB:Solexa-272222 PI:0 DT:2014-08-20T00:00:00-0400 SM:NA12878 CN:BI
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