standard-bin.json~

{
     "bin": {
        "NOVOALIGN": "/usr/local/apps/novocraft/3.02.10/novoalign",
        "NOVOSORT": "/usr/local/apps/novocraft/3.02.10/novosort",
#        "ANNOVAR1": "/usr/local/apps/ANNOVAR/2014-07-14/convert2annovar.pl", 
#        "ANNOVAR2": "/usr/local/apps/ANNOVAR/2014-07-14/table_annovar.pl", 
        "ANNOVAR1": "/usr/local/apps/ANNOVAR/2015-03-22/convert2annovar.pl",
        "ANNOVAR2": "/usr/local/apps/ANNOVAR/2015-03-22/table_annovar.pl",
        "INDEXBAM": "java -jar /usr/local/apps/picard/1.129/picard.jar BuildBamIndex", 
        "COVCALC": "QC/Coverage_calc4.pl", 
        "COVFREQ": "/data/CCBR/local/lib/Cov_Frequency_targeted.R",
        "GATK": "java -Xmx64g -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/GATK/3.5-0/GenomeAnalysisTK.jar", 
        "MARKDUPS": "java -Xmx16g -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/picard/1.129/picard.jar MarkDuplicates", 
        "PICARD1": "java -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/picard/1.129/picard.jar AddOrReplaceReadGroups", 
        "PICARD2": "java -Xmx4G -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/picard/1.129/picard.jar CollectInsertSizeMetrics", 
        "PICARD3": "/ngs/bin/jdk1.8.0_25/bin/java -jar /ngs/bin/picard-tools-1.119/CreateSequenceDictionary.jar",
        "PICHIST": "/data/CCBR/local/lib/picardhist.R", 
        "QCAL": "/data/CCBR/local/lib/qcalplot.R", 
        "READDIST": "/data/CCBR/local/lib/ReadDist.R", 
        "VARSCAN": "java -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/varscan/2.3.6/VarScan.v2.3.6.jar",
        "NGSQCTOOLKIT": "/usr/local/apps/ngsqctoolkit/2.3.3/QC/IlluQC.pl",
        "TRIMMOMATIC": "java -Xmx8g  -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar",
        "FASTQC": "export JAVA_OPTS='-Djava.io.tmpdir=/lscratch/${SLURM_JOBID}; /usr/local/apps/fastqc/0.11.2/fastqc",
        "SAMTOOLS": "/usr/local/apps/samtools/samtools-0.1.18/samtools",
        "BAMTOOLS": "/usr/local/apps/bamtools/2.3.0/bin/bamtools",
        "BEDTOOLS": "/usr/local/apps/bedtools/2.19.0/bin/bedtools",
        "QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/${SLURM_JOBID}'; /data/CCBR/local/bin/qualimap_v2.0.1/qualimap --java-mem-size=64G",
        "STAR": "/usr/local/apps/STAR/2.4.0h/bin/Linux_x86_64/STAR",
        "SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/snpEff/4.1c/snpEff.jar",
        "SNPSIFT": "java -Xmx24g -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/snpEff/4.1c/SnpSift.jar",
        "FIRSTANNO": "Scripts/vcfAnnFirst_snpEff.py",
        "MUTECT": "module load java/1.7.0_25; java -Xmx16g -Djava.io.tmpdir=/lscratch/${SLURM_JOBID} -jar /usr/local/apps/muTect/2014-12-15/muTect-1.1.7.jar",
        "SVDETECT": "/data/CCBR/local/apps",
        "BICSEQ": "/data/CCBR/local/apps/BIC-seq.pl",
        "BWA": "/usr/local/apps/bwa/0.7.10/bwa"

    }
}