GATK commands for mutect2
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13 months ago
Monisha • 0

What are the commands used to perform GATK using mutect2?

Mutect2 GATK • 760 views
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what did you find so far ?

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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!!!

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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

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