Error in Gatk(discoveryVarient.sh)

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3.6 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?

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ADD COMMENT • link 3.6 years ago by zaisha.jotyalam • 0

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where did you find this discoveryVariant.sh ?

ADD REPLY • link 3.6 years ago by Pierre Lindenbaum 161k

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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 ?

ADD REPLY • link 3.6 years ago by GenoMax 142k

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It was included in GATK.

ADD REPLY • link 3.6 years ago by zaisha.jotyalam • 0

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