To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

GATK4-beta Mutect2 input and samplenames

I'm using paired tumor-normal samples, and since the command line parameters have changes, I wanted to make sure that I'm defining my input files and sample names correctly. The command I use is

java -Xmx{params.xmx} Xms{params.xms} -jar {params.GATK} Mutect2 --reference {input.REF} --intervals {input.INTERVAL_LIST} --input {input.NORMAL_BAM} --input {input.TUMOR_BAM} --tumorSampleName {params.TUMOR_BAM_SAMPLE_NAME} O {output.VCF}

TUMOR_BAM_SAMPLE_NAME is the name of the sample as in the BAM header (SM). Is it necessary to define the sample name of the normal sample, when using paired samples?

From the help:
--input,-I:String. BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required.
--tumorSampleName,-tumor:String. BAM sample name of tumor Required.
--normalSampleName,-normal:String. BAM sample name of tumor Default value: null.

Best Answer


Sign In or Register to comment.