I'm using GATK v220.127.116.11 running this:
gatk --java-options -Xmx4g HaplotypeCaller -R ref.fasta -I input.bam -O output.vcf.gz
I get an 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.
But my input BAM file only has one reference in it. The reference name is ok, according to the SAM standard regex. There is also only a single read group.
When I repeat the above call and put --sample-name REFNAME on the command line, I get another error:
A USER ERROR has occurred: Argument --sample_name has a bad value: Specified name does not exist in input bam files
But the sample name I give on the command line matches the one in my BAM file. So on the one hand GATK is complaining that my BAM file has multiple samples (I assume that means multiple references) but on the other hand when I give it a sample name it says it doesn't exist.
I have checked my BAM file to make sure that only one reference occurs in (SAM) field 3.
BTW, regarding the second error message above, it would be useful if it 1) said --sample-name instead of --sample_name (I tried to find this in the GATK repo, but could not), 2) printed out the value it was looking for (so that I can see that it's looking for what I gave it on the command line and not something else, which could occur to due to a bug in GATK), and 3) told me what "samples" it finds in the BAM file so that I could see what GATK thinks is in there. The second and third of these suggestions would potentially make it easier for a regular user to resolve an issue like this.
Thanks for any help (and for GATK)!
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