What are the commands used to perform GATK using mutect2?
what did you find so far ?
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!!!
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
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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