We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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: https://github.com/broadinstitute/gatk/blob/master/scripts/mutect2_wdl/mutect2.wdl .

My call to Mutect2 looks like this (the following is from exec.sh, 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.