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'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-
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,


Best Answer


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