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standard-bin.json.bak
executable file
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standard-bin.json.bak
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{
"bin": {
"NOVOALIGN": "/usr/local/apps/novocraft/3.04.04/novoalign",
"NOVOSORT": "/usr/local/apps/novocraft/3.04.04/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/$SLURM_JOBID -jar /usr/local/apps/GATK/3.5-0/GenomeAnalysisTK.jar",
"MARKDUPS": "module load picard/2.1.1; java -Xmx16g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar MarkDuplicates",
"PICARD1": "module load picard/2.1.1; java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups",
"PICARD2": "module load picard/2.1.1; java -Xmx4G -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar CollectInsertSizeMetrics",
"PICARD3": "/ngs/bin/jdk1.8.0_25/bin/java -jar /ngs/bin/picard-tools-1.119/CreateSequenceDictionary.jar",
"PICHIST": "/data/CCBR/local/lib/picardhist.R",
"QCAL": "/data/CCBR/local/lib/qcalplot.R",
"READDIST": "/data/CCBR/local/lib/ReadDist.R",
"VARSCAN": "java -Djava.io.tmpdir=/lscratch/$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/0.11.5/fastqc",
"FASTQC": "/usr/local/apps/fastqc/0.11.5/fastqc",
"SAMTOOLS": "/usr/local/apps/samtools/1.3.1/bin/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/4.2/snpEff.jar",
"SNPSIFT": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/SnpSift.jar",
"FIRSTANNO": "Scripts/vcfAnnFirst_snpEff.py",
"MUTECT": "module load java/1.7.0_25; java -Xmx16g -Djava.io.tmpdir=/lscratch/$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",
"FASTQ_SCREEN": "/data/CCBR/apps/fastq_screen_v0.6.3/fastq_screen"
}
}