We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
CGA WES pipeline ICE intervals
I'm trying to use the CGA WES pipeline. I cloned the workspace
And imported my data and set up the method config for my samples. But I went to launch the analysis and got this failed message:
My WES samples were done on the Illumina ICE platform. My understanding from the CGA WES user guide is that the workspace has two files in the bucket, one for Agilent ("AGILENT_TARGET_INTERVALS") and one for ICE ("ICE_TARGET_INTERVALS").
The default in the method config was the Agilent, so I changed the baitIntervals and targetIntervals variables to workspace.ICE_BAIT_INTERVALS and workspace.ICE_TARGET_INTERVALS respectively, but it doesn't seem to work when I launch the analysis.
Is there another step I need to include? Thanks!!