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Last pushed: a day ago
Short Description
somaticseq (project site: https://github.com/bioinform/somaticseq)
Full Description
  • The base image also includes an MIT licensed part of GATK v3.4 at /opt/GATK (for GATK CombineVariants).

    Example command:

    docker run --rm -v $PATH/TO/DATA/:/mnt -u $UID lethalfang/somaticseq:latest \
    /opt/somaticseq/SomaticSeq.Wrapper.sh \
    --gatk /opt/GATK/GenomeAnalysisTK.jar \
    --mutect2 /mnt/GATK3-MuTect2.vcf \
    --varscan-snv /mnt/VarScan2.snp.vcf \
    --varscan-indel /mnt/VarScan2.indel.vcf \
    --jsm /mnt/JointSNVMix2.vcf \
    --sniper /mnt/SomaticSniper.vcf \
    --vardict /mnt/VarDict.vcf \
    --muse /mnt/MuSE.vcf \
    --lofreq-snv /mnt/LoFreq.snvs.vcf.gz \
    --lofreq-indel /mnt/LoFreq.indels.vcf.gz \
    --scalpel /mnt/Scalpel.vcf \
    --strelka-snv /mnt/results/variants/somatic.indels.vcf.gz \
    --strelka-indel /mnt/results/variants/somatic.snvs.vcf.gz \
    --genome-reference /mnt/GRCh38.fa \
    --cosmic /mnt/COSMIC/v77_coding.hg38.vcf \
    --dbsnp /mnt/dbSNP/dbsnp_144.hg38.vcf \
    --inclusion-region /mnt/Capture_Regions.bed \
    --exclusion-region /mnt/Blacklist_Regions.bed \
    --tumor-bam /mnt/tumorSample.bam \
    --normal-bam /mnt/normalSample.bam \
    --output-dir /mnt/SomaticMutationCalls
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Owner
lethalfang

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