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Mutect2 does not recognize reference sequence

Hi GATK team,

I'm trying to run the Mutect2 pipeline on build 38 WGS CRAM files. I am using something very similar to this WDL: .

My call to Mutect2 looks like this (the following is from, generated by Cromwell):

gatk --java-options "-Xmx4g" Mutect2 \
$tumor_command_line \
$normal_command_line \
--germline-resource /cromwell_root/somatic-workspace/sites.vcf.gz \
-pon /cromwell_root/somatic-workspace/PON.vcf \
-L /cromwell_root/somatic-workspace/Mutect2/8f8e9314-936a-45f4-91cb-878530214146/call-SplitIntervals/glob-6f4bc12a708659d4f5f3eecd1cdffff7/0000-scattered.intervals \
--af-of-alleles-not-in-resource 0.000006 \
--max-population-af 0.001 \
-R /cromwell_root/reference/hs38DH.fa \
-O "output.vcf"

I am running this without specifying the "normal_bam" option; i.e., I only specify the tumor_bam as my CRAM file.

Despite the fact that I am specifying the reference, I receive the following error:

"A USER ERROR has occurred: A reference file is required when using CRAM files."

Am I specifying the call incorrectly?


Best Answer


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