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3.5 years ago
zaisha.jotyalam
•
0
I have downloaded the Gatk from Broadinstitute. Inside the folder, there is a script discoveryVariant.sh This script is in /home/user/gatk/scripts/sv/stepByStep/. As required parameters, I have edited it but there are continuous errors. They are asking for- 1.In 5 number line in the script, there is an error and 2.Another error is line number 15(CLUSTER_NAME) 3.The last error was in line 16(MASTER_NODE)
Can anyone please suggest me how to solve this errors?
where did you find this discoveryVariant.sh ?
It is included in GATK:
gatk-4.x.x.x/scripts/sv/stepByStep/discoverVariants.sh
Looks like the script is for running on a Hadoop cluster. Do you have access to one zaisha.jotyalam ?
It was included in GATK.