Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

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.