GATK issue in running Mutect2
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20 months ago

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 : It says reference genome doesn't exist in the particular folder, but it is

next-gen snp • 833 views
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from the place where you're invoking gatk, what is the output of ls GRCh38.p13.genome.fa ?

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

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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 = []

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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

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19 months ago
spriyansh29 ▴ 30

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

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19 months ago
2nelly ▴ 310

"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.

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