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 :
•
written
by
jyotsana18237 •
2 answers
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
"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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from the place where you're invoking gatk, what is the output of
ls GRCh38.p13.genome.fa?I am getting the name of the file i.e "GRCh38.p13.genome.fa"
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 = []
HOW ? WHAT WAS THE ERROR ?
known error