I am running the HaplotypeCaller as a part of the GATK pipeline on a single BAM file. I keep getting the error:
A USER ERROR has occurred: Argument --emitRefConfidence 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.
However, I am fairly confident that there is only one sample in the BAM file. I tried neglecting the
-ERC GVCF as per some suggestions (haplotypecaller can not run in single bam file) but get this message instead:
htsjdk.samtools.util.RuntimeIOException: Unable to close index for file: ... ... Caused by: java.io.IOException: Terminator block not found after closing BGZF file: ...
However, as some people suggested (https://gatkforums.broadinstitute.org/gatk/discussion/11202/haplotypecaller-error-in-the-middle-of-processing), I increased the memory to over 100G and it didn't solve the problem.
Does anyone have any suggestions?