'Unable to access jarfile MuTect2' Could you explain me where's the problem?
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:
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-220.127.116.11 source .bashrc
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,