Global config

= Pipeline Global Configuration =

export tools_dir="~/tools" export resources="~/R" export PATH=$PATH:$resources export bwa="${tools_dir}/bwa-0.7/bwa" export hg19_ref="${tools_dir}/bwa-0.7/database/hg19/ucsc.hg19.fasta" export REF=$hg19_ref export fai="${tools_dir}/bwa-0.7/database/hg19/ucsc.hg19.fasta.fai" export samtools="${tools_dir}/samtools-0.1.18_x86_64-linux/samtools" export samtoolspath="${tools_dir}/samtools-0.1.18_x86_64-linux" export classpath=$classpath:$samtoolspath export bamtools="${tools_dir}/bamtools-fffb428/bin/bamtools" export intersectBed="${tools_dir}/bedtools/bin/intersectBed" export gatk="${tools_dir}/GenomeAnalysisTK-2.6/GenomeAnalysisTK.jar" export gatk_analyzecovar="${tools_dir}/   \ GenomeAnalysisTK-2.6/AnalyzeCovariates.jar" export DBSNP="${tools_dir}/files/dbSNP135/dbsnp_137.vcf" export DBSNP_idx="${tools_dir}/files/dbSNP135/dbsnp_137.vcf.idx" export REFSEQ="${tools_dir}/files/refgene/refgene-hg19/refGene-converted.rod" export REFSEQ_idx="${tools_dir}/files/refgene/refgene-hg19/refGene-converted.rod.idx" # format: http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK # http://www.nimblegen.com/products/seqcap/arrays/exome/index.html export # http://www.nimblegen.com/products/seqcap/ez/v2/index.html # http://www.nimblegen.com/products/seqcap/ez/v3/index.html
 * 1) script and tools folder
 * 1) bwa setting (ref Lexicographically sorted )
 * 1) human genome ref
 * 1) samtools
 * 1) bamtools
 * 1) bedtools
 * 1) GATK
 * 1) DBSNP
 * 1) REFSEQ
 * 1) Exon target interval file format:
 * 1) Data source for Nimblegen:

ExonFile="${tools_dir}/files/exon.target.interval_list" export picard="${tools_dir}/picard-tools-1.56" export classpath=$classpath:$picard export heap=8000 export CPUs=3 < Back to Whole Exome Sequencing Analysis Pipeline
 * 1) PICARD
 * 1) Java config
 * 1) CPUs