GATK issue in running Mutect2

Question

[jyotsana18237]

I am new to GATK, I want to run the Mutect2 tool for identifying somatics varients. The command which I run is:

" gatk Mutect2 -R GRCh38.p13.genome.fa -I tumor.bam -I normal.bam -O out1.vcf.gz"

Can some please assist me where I am going wrong? The error message I am getting is :

[Pierre Lindenbaum]

from the place where you're invoking gatk, what is the output of ls GRCh38.p13.genome.fa ?

[jyotsana18237]

I am getting the name of the file i.e "GRCh38.p13.genome.fa"

[jyotsana18237]

The above error gets resolved, now I am facing a new error. It says "A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found."

The read contigs list is empty reads contigs = []

[Pierre Lindenbaum]

The above error gets resolved,

HOW ? WHAT WAS THE ERROR ?

"A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found

known error

Answer 1

[sp29]

If you are running the Mutect2 with a tumour-matched normal setting, you need to explicitly supply the normal sample name. You should first run GetSampleName -I normal.bam -O name.out. This will give you the name of your normal sample in a file "name.out", which you have to pass in Mutect2. So your command would be,

gatk Mutect2 -R GRCh38.p13.genome.fa \

-I tumour.bam \

-I normal.bam \

-normal "The name you get in the name.out" \

-O out1.vcf.gz

Answer 2

[2nelly]

"A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found."

That means alignment was done with different reference genome file. Check the chromosomes names in the header of your bam files and those in your reference genome. They should be different.