To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

MuTect2 Seems to lose a lot of mutations.

I use Mutect2 (tumor only mode) to find somatic mutation, but some position was not able find mutations.
I have attached some IGV figures in the regions where MuTect2 has missed somatic mutations (Top is bam file to input Mutect2, bottom is bamout file from Mutect2).
Some are too obvious, and cannot understand why MuTect2 does not identify them as mutation.
I think I might need to modify some parameters when I run MuTect.
Which parameter can I adjust?

The command is here:
java -Xmx4g -jar /GATK3.7-0/GenomeAnalysisTK.jar -T MuTect2 -L Target.bed -R hg19.fasta
-I:tumor test.bam --dbsnp All_20170403.vcf.gz --cosmic CosmicCodingMutsGRCh37v81.vcf
-dfrac 1 --maxReadsInRegionPerSample 100000 --minPruning 1 --artifact_detection_mode
--useNewAFCalculator -o test.vcf -bamout test.bam -log test.log

BWA mem 0.7.12
GATK 3.7/4.0



Best Answer


Sign In or Register to comment.