The GATK "The given bam input has no sample names." error

Question

[Begonia_pavonina]

for f in MINIMAP BWA ;
do
    ~/gatk-4.2.0.0/gatk HaplotypeCaller --reference  /home/tmichel/projects/rbge/HybSeq_thibauld/reference_genomes/Begonia_loranthoides_scaffold.fasta --input  Hillebrandia_sorted.$f.bam  --output Hillebrandia.$f.g.vcf.gz --emit-ref-confidence GVCF ; 
done

I have used GATK to call variants in BAM files files with both minimap2 and bwa mem with the following script:

~/gatk-4.2.0.0/gatk HaplotypeCaller \
--reference  REF.fasta \
--input  INPUT.bam  \
--output OUTPUT.g.vcf.gz \
--emit-ref-confidence GVCF

But the following error popped:

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.

I have then check the samples names in my BAM file:

 ~/gatk-4.2.0.0/gatk GetSampleName \
        -I INPUT.bam

But the following error popped:

A USER ERROR has occurred: Bad input: The given bam input has no sample names.

It is a bit odd, as I have processed other samples through the PALEOMIX pipeline, using BWA as well for alignement, and never had this issue. Has anyone here experienced the same issue?

Answer 1

[Pierre Lindenbaum]

your bam is missing a 'SM' section in the read groups. This should have been specified when mapping with bwa. https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups

[Begonia_pavonina]

Thank you for the info! Very curious Minimap and BWA do not include this field as default in the sam file. I will try to find the options to do so.

[samuel.a.odonnell]

You can also add the sample name with gatk with AddOrReplaceReadGroups

[Begonia_pavonina]

Thank you. For some reason, although the command is working, no name is detected using GetSampleName. I hope to find the proper option to name the sample while using BWA or Minimap to align the reads. Let me know if you are using them!

[GenoMax]

This thread --> Can't add read group correctly to minimap2 sam alignmnet shows you how to add read groups in minimap2 and bwa commands. The thread is about something else but just take a look at the original post for how to specify read groups with minimap2 and @h.mons comment to see how to do it for bwa,