If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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


Sign In or Register to comment.