Hello,
I'd like to detect somatic mutations using Gatk Mutect2, I have nice Illumina WES experiment. Then publish my results with gatk tool citation of course. Unfortunately a problem has occurred in contrast to other NGS analysis tools.
I try to follow this tutorial:
https://software.broadinstitute.org/gatk/documentation/article?id=9183
I downloaded latest version of gatk, archive has been unzipped and also I add path to gath to $PATH:
export PATH=$PATH:/home/admin/soft/gatk-4.0.2.1
source .bashrc
After running gatk
I see:
Usage template for all tools (uses --spark-runner LOCAL when used with a Spark tool)
gatk AnyTool toolArgs
Usage template for Spark tools (will NOT work on non-Spark tools)
gatk SparkTool toolArgs [ -- --spark-runner <LOCAL | SPARK | GCS> sparkArgs ]
(...)
So I think that works.
Based on tutorial I tried to run --artifact_detection_mode
with my files, it looks like this:
java -jar $GATK \
-T MuTect2 \
-I:tumor ~/Desktop/bams/sample1.bam \
--dbsnp ~/refs/All_20170710.vcf.gz \
--artifact_detection_mode \
-o sample1_forpon.vcf.gz \
-R ~/refs/Homo_sapiens.GRCh37.75.dna_sm.primary_assembly.fasta
As a result I have only:
Error: Unable to access jarfile MuTect2
I'd be very grateful if someone would shed a light in this case.
Thank You and best regartds,
Adam