GATK commands for mutect2

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2.9 years ago

Monisha • 0

What are the commands used to perform GATK using mutect2?

Mutect2 GATK • 1.4k views

ADD COMMENT • link updated 2.0 years ago by Ram 44k • written 2.9 years ago by Monisha • 0

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what did you find so far ?

ADD REPLY • link 2.9 years ago by Pierre Lindenbaum 164k

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java -Xmx4G -jar gatk-package   Mutect2 -R (path and name of genome file) -I (path and name of validated sort.bam file) -o (path and name of validated sort.vcf file)

I have given this command for the generation of vcf file using Mutect2(GATK)

is this command correct please help!!!

ADD REPLY • link updated 2.0 years ago by Ram 44k • written 2.9 years ago by Monisha • 0

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You can find detailed help on how to use mutect2 here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2

There is also a FAQ: https://gatk.broadinstitute.org/hc/en-us/articles/360050722212-FAQ-for-Mutect2

ADD REPLY • link 2.9 years ago by GenoMax 147k

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What is tumor.bam ? And ref.fasta is not accepting in gatk . And I have taken sam tool files as input to gatk Mutect2

ADD REPLY • link 2.9 years ago by Monisha • 0

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