Hey everyone, I'm an aspiring beginner in the gatk world and would like to start using MuTect2.
Super basic commands are not working though and I can't figure out why. Please help me :)
a) GATK version used
b) Exact GATK commands used
gatk Mutect2 -R ref.fasta -I tumor.bam -O unfiltered.vcf
Took this example comment from this tutorial: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132. Seems like the GATK doesn't recognise the Mutect2 tool. What is missing?
In the path I have the ref.fasta and tumor.bam, named exactly like that.
c) The entire error log if applicable.
-bash: gatk: command not found
Please sign in to leave a comment.