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configure_dir.R
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configure_dir.R
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fastqc = '/home/huw/program/FastQC/fastqc'
hsaMethylBaitIntervalOrig='/home/huw/program/truseq-methyl-capture-epic-manifest-file.bed'
hsaMethylBaitInterval ='/home/huw/program/truseq-methyl-capture-epic-manifest-file-bait.interval'
hsaMethylTargetInterval = '/home/huw/program/truseq-methyl-capture-epic-manifest-file-plusminus5bp.interval'
options(scipen=999)
system(paste0('cp /home/huw/program/truseq-methyl-capture-epic-header.txt ', hsaMethylBaitInterval))
tmp = fread(hsaMethylBaitIntervalOrig)
tmp = tmp[order(V1),]
library(tibble)
tmp = add_column(tmp, string = "+", .after = 3)
tmp[, V1:=sub("chr", "", V1)]
fwrite(tmp, file=hsaMethylBaitInterval, quote=F, sep="\t", col.names=F, append=T)
write.table(as.data.frame(tmp), file=hsaMethylBaitInterval, quote=F, sep="\t", col.names=F, append=T, row.names=F)
tmp[, V2:=V2-5]
tmp[, V3:=V3+5]
head(tmp)
tmp[, V1 := as.character(V1)]
tmp[, V2 := as.character(V2)]
tmp[, V3 := as.character(V3)]
tmp[, V4:=paste0("chr", V1, "_", V2, "-", V3)]
system(paste0('cp /home/huw/program/truseq-methyl-capture-epic-header.txt ', hsaMethylTargetInterval))
write.table(as.data.frame(tmp), file=hsaMethylTargetInterval, quote=F, sep="\t", col.names=F, append=T, row.names=F)
rm(tmp)
bismarkGRCh37 = '/ifs/work/solitlab/huw/study/db/hsa/grch37_bismark'
bismark = '/home/huw/program/Bismark'
methylTarget = '/home/huw/program/truseq-methyl-capture-epic-manifest-file.bed'
SOAPHLA = '/home/huw/program/SOAP-HLA'
bamReadCount = '/home/huw/local/bam-readcount'
IEDBMHC1 = '/home/huw/program/mhc_i'
IEDBMHC1 = '/home/huw/program/mhc_ii'
pvacseq = '/home/huw/program/anaconda3/bin/pvacseq'
tmpdir = '/scratch/huw'
polysolver = '/home/huw/program/polysolver'
ponfile = '/home/huw/program/pon56Sample.vcf.gz'
make.trinuc = '/home/huw/program/make_trinuc_maf.py'
mutsig = '/opt/common/CentOS_6-dev/mutsig/cv-1.4/'
belly2 = '/home/huw/program/delly_v0.7.7_linux_x86_64bit'
exeDir = '/ifs/work/solitlab/huw/program/socciCode/Pipelines/CBE/Variant/variants_pipeline/'
targetsDir = '/ifs/work/solitlab/huw/program/socciCode/Pipelines/CBE/Variant/variants_pipeline/targets/'
facets = '/ifs/work/solitlab/huw/program/socciCode/Pipelines/CBE/Variant/variants_pipeline/facets'
vepDir = '/ifs/work/solitlab/huw/program/socciCode/Pipelines/CBE/Variant/variants_pipeline/vep'
dataDir = '/ifs/work/solitlab/huw/program/socciCode/Pipelines/CBE/Variant/variants_pipeline/data'
ConvertQualityScore = '/home/huw/program/ConvertQualityScore'
STAR = '/home/huw/program/STAR-STAR_2.5.0a/bin/Linux_x86_64_static/STAR'
STAR_DIR = '/home/huw/program/STAR-STAR_2.5.0a/bin/Linux_x86_64_static'
RSEM = '/opt/common/CentOS_6/rsem/RSEM-1.2.25/'
KALLISTO = '/home/huw/local/bin/kallisto '
##STAR = '/opt/common/CentOS_6/star/STAR-STAR_2.5.0a/bin/Linux_x86_64/STAR'
samtools = '/opt/common/CentOS_6-dev/bin/current/samtools'
samtoolsdir = '/opt/common/CentOS_6-dev/samtools/samtools-1.3.1'
sambamba = '/home/huw/program/sambamba'
java = '/home/huw/program/jdk7/bin/java'
java = '/opt/common/CentOS_6-dev/java/jdk1.8.0_31/bin/java'
picard = '/home/huw/program/picard.jar'
htseqcountexe = '/home/huw/local/bin/htseq-count'
NGSPLOTexe = '/home/huw/program/ngsplot/bin/ngs.plot.r'
NGSFilter = '/home/huw/program/ngs-filters/'
QSUB = '/common/sge/bin/lx24-amd64/qsub'
BSUB = '/common/lsf/9.1/linux2.6-glibc2.3-x86_64/bin/bsub'
trim_galore = '/home/huw/program/trim_galore'
bowtie2 = '/home/huw/program/bowtie2/bowtie2'
bowtie2dir = '/home/huw/program/bowtie2'
macs14 = '/home/huw/local/bin/macs14'
macs2 = '/home/huw/local/bin/macs2'
homerFindMotif = '/home/huw/program/homer/bin/findMotifsGenome.pl'
homerAnnotatePeaks = '/home/huw/program/homer/bin/annotatePeaks.pl'
tssCounts = '/home/huw/program/tsscounts.pl'
bwa = '/home/huw/program/bwa-0.7.12/bwa '
bedtools = '/home/huw/program/bedtools/bin'
bam2bigwig = '/home/huw/program/bam2bigwig.sh'
annotationFilter = '/home/huw/program/annotationFilter.pl'
enhancerMm10Bed = '/ifs/work/solitlab//huw/study/db/mmu/dna/Mus_musculus.GRCm38.79.enhancer.bed'
enhancerMm9Bed = '/home/program/PLtest/Enhancers_mm9_CreyghtonPNAS/PutativeEnhancers_mm9_5types_SortMerge300_noPromOL_GT50bp.txt'
tssMm9Bed = '/home/huw/program/PLtest/refFlat_mm9_TSSpm2kbSORTED.txt'
tssMm10Bed = '/ifs/work/solitlab//huw/study/db/mmu/dna/Mus_musculus.GRCm38.79.chr.symbol.tss2kb.bed'
genomeMm9Bowtie2 = '/ifs/work/solitlab//huw/study/db/mmu/mm9-bowtie2/mm9'
genomeMm9StarDir = '/ifs/work/solitlab//huw/study/db/mmu/mm9_star'
genomeMm9GTF = '/ifs/work/solitlab//huw/study/db/mmu/dna/Mus_musculus.NCBIM37.67.chr.gtf'
genomeMm10Bowtie2 = '/ifs/work/solitlab//huw/study/db/mmu/mm10-bowtie2/mm10'
genomeMm10StarDir = '/ifs/work/solitlab//huw/study/db/mmu/mm10star'
genomeMm10GTF = '/ifs/work/solitlab//huw/study/db/mmu/dna/Mus_musculus.GRCm38.79.chr.gtf'
mm10chromsize = '/ifs/work/solitlab//huw/study/db/mmu/dna/Mus_musculus.GRCm38.79.chrom.size'
ABRA = '/opt/common/CentOS_6/abra2/abra2-2.07'
BCFTOOLS = '/opt/common/CentOS_6/bcftools/bcftools-1.2/bin'
BEDTOOLS = '/opt/common/CentOS_6/bedtools/bedtools-2.22.0/bin'
BWA = '/opt/common/CentOS_6/bwa/bwa-0.7.12/bwa'
CUTADAPT = '/opt/common/CentOS_6/cutadapt/cutadapt-1.9.1/bin/cutadapt'
DELLY = '/opt/common/CentOS_6/delly/delly_v0.6.1'
dRANGER = '/opt/common/CentOS_6/dranger/dRanger_annotate_v2.0'
FACETS_SUITE = '/home/huw/program/facets-suite-1.0.1'
FACETS_LIB = '/opt/common/CentOS_6-dev/facets_lib/facets-0.5.6'
FIXMULTIINDEL = '/opt/common/CentOS_6/FixMultiInDel/FixMultiInDel-2.0.1'
GATK = '/home/huw/program/GenomeAnalysisTK-3.8-0-ge9d806836'
GATK4 = '/home/huw/program/gatk-4.0.2.1/gatk'
#GATK4 = '/home/huw/program/gatk-4.0.2.1/gatk-package-4.0.2.1-local.jar'
gnomadfile = '/home/huw/af-only-gnomad.raw.sites.b37.vcf.gz'
JAVA = '/opt/common/CentOS_6/java/jdk1.8.0_31/bin'
JAVA7_MUTECT = '/opt/common/CentOS_6/java/jdk1.7.0_75/bin'
MCR = '/opt/common/CentOS_6/matlab/v81'
MUTECT = '/opt/common/CentOS_6/muTect/muTect-1.1.7'
PERL = '/opt/common/CentOS_6/perl/perl-5.22.0/bin'
PERL = '/home/huw/local/perl/perl-5.26.0/bin'
PICARD = '/home/huw/program/picard.jar'
PYTHON = '/opt/common/CentOS_6/python/python-2.7.8/bin/python'
R = '/opt/common/CentOS_6/R/R-3.1.2/bin'
SAMTOOLS = '/opt/common/CentOS_6/samtools/samtools-1.2'
SCALPEL = '/opt/common/CentOS_6/scalpel/scalpel-0.2.2'
SOMATICSNIPER = '/opt/common/CentOS_6/somaticsniper/somatic-sniper-1.0.4'
STRELKA = '/opt/common/CentOS_6/strelka/strelka_1.0.11'
TABIX = '/opt/common/CentOS_6/samtools/samtools-1.2/htslib-1.2.1'
VARSCAN = '/opt/common/CentOS_6/varscan/v2.3.7'
VCF2MAF = '/home/huw/program/vcf2maf-1.6.14'
VCFTOOLS = '/opt/common/CentOS_6-dev/vcftools/v0.1.14/bin'
VEP = '/opt/common/CentOS_6-dev/vep/v86'
VEPv88 = '/opt/common/CentOS_6-dev/vep/v88/variant_effect_predictor.pl'
VEP_plugins = '/home/huw/program/VEP_plugins'
VIRMID = '/opt/common/CentOS_6/virmid/Virmid-1.1.1'
WES_FILTER = '/opt/common/CentOS_6/wes-filter/wes-filters-1.1.3'
CMOBIN = '/opt/common/CentOS_6-dev/python/python-2.7.10/bin/'
B37_BWA_INDEX = '/ifs/depot/assemblies/H.sapiens/b37/index/bwa/0.7.12/b37.fasta'
B37_FASTA = '/ifs/depot/assemblies/H.sapiens/b37/b37.fasta'
B37_FAI = '/ifs/depot/assemblies/H.sapiens/b37/b37.fasta.fai'
B37_MM10_HYBRID_BWA_INDEX = '/ifs/depot/assemblies/hybrids/H.sapiens_M.musculus/b37_mm10/index/bwa/0.7.12/b37_mm10.fasta'
B37_MM10_HYBRID_FASTA = '/ifs/depot/assemblies/hybrids/H.sapiens_M.musculus/b37_mm10/b37_mm10.fasta'
B37_MM10_HYBRID_FAI = '/ifs/depot/assemblies/hybrids/H.sapiens_M.musculus/b37_mm10/b37_mm10.fasta.fai'
HG19_BWA_INDEX = '/ifs/depot/assemblies/H.sapiens/hg19/index/bwa/0.7.4-r385/hg19.fasta'
HG19_FASTA = '/ifs/depot/assemblies/H.sapiens/hg19/hg19.fasta'
HG19_FAI = '/ifs/depot/assemblies/H.sapiens/hg19/hg19.fasta.fai'
HG19_MM10_HYBRID_BWA_INDEX = '/ifs/depot/assemblies/hybrids/H.sapiens_M.musculus/hg19_mm10/index/bwa/0.7.8/hg19_mm10.fasta'
HG19_MM10_HYBRID_FASTA = '/ifs/depot/assemblies/hybrids/H.sapiens_M.musculus/hg19_mm10/hg19_mm10.fasta'
HG19_MM10_HYBRID_FAI = '/ifs/depot/assemblies/hybrids/H.sapiens_M.musculus/hg19_mm10/hg19_mm10.fasta.fai'
MM9_BWA_INDEX = '/ifs/depot/assemblies/M.musculus/mm9/index/bwa/0.7.4-r385/mm9.fasta'
MM9_FASTA = '/ifs/depot/assemblies/M.musculus/mm9/mm9.fasta'
MM9_FAI = '/ifs/depot/assemblies/M.musculus/mm9/mm9.fasta.fai'
MM10_BWA_INDEX = '/ifs/depot/assemblies/M.musculus/mm10/index/bwa/0.7.8/mm10.fasta'
MM10_FASTA = '/ifs/depot/assemblies/M.musculus/mm10/mm10.fasta'
MM10_FAI = '/ifs/depot/assemblies/M.musculus/mm10/mm10.fasta.fai'
clipR1 = 'AGATCGGAAGAGCACACGTCT'
clipR2 = 'AGATCGGAAGAGCACACGTCT'
bqtrim = '3'
## for homer annotatePeaks.pl mm10
homerMm10AnnotationFile = '/ifs/work/solitlab//huw/study/db/mmu/dna/Mus_musculus.GRCm38.79.chr.gtf.annotations.final.txt'
genomeHg19Bwa = '/ifs/work/solitlab//huw/study/db/hsa/hg37-bwa/hg37 '
genomeHg19StarDir = '/ifs/work/solitlab//huw/study/db/hsa/hg37star'
genomeHg19Bowtie2 = '/ifs/work/solitlab//huw/study/db/hsa/hg37bowtie2/hg37'
genomeHg38Bowtie2 = '/ifs/work/solitlab//huw/study/db/hsa/hg38_bowtie2/hg38'
genomeHg19GTF = '/ifs/work/solitlab//huw/study/db/hsa/dna/Homo_sapiens.GRCh37.75.gtf'
hg19chromsize = '/ifs/work/solitlab//huw/study/db/hsa/dna/Homo_sapiens.GRCh37.75.chrom.size'
genomeGRCh37Fasta = '/ifs/work/solitlab/huw/study/db/hsa/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa'
genomeGRCh37StarDir = '/ifs/depot/assemblies/H.sapiens/b37/index/star/2.4.1d/gencode/v18/overhang49 /ifs/work/solitlab/huw/park/study/hiseq/chipseq/template.conf'
genomeGRCh38GTF = '/ifs/work/solitlab/huw/study/db/hsa/dna/Homo_sapiens.GRCh38.88.gtf'
genomeGRCh38Fasta = '/ifs/work/solitlab/huw/study/db/hsa/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa'
genomeGRCh38StarDir = '/ifs/work/solitlab/huw/study/db/hsa/hg38_star'
genomeGRCh38Rsem = '/ifs/work/solitlab/huw/program/RSEM_tutorial/ref/GRCh38/GRCh38'
RSEM_REF = '/ifs/work/solitlab/huw/program/RSEM_tutorial/ref/GRCh38/GRCh38'
genomeGRCh38Kallisto = '/ifs/work/solitlab/huw/study/db/hsa/hg38_kallisto/kallisto_GRCh38'
genomeGRCm38Fasta = '/ifs/work/solitlab/huw/study/db/mmu/dna/Mus_musculus.GRCm38.79.dna.primary_assembly.chr.fa'
genomeGRCm38GTF = '/ifs/work/solitlab/huw/study/db/mmu/dna/Mus_musculus.GRCm38.79.chr.gtf'
genomeGRCm38Rsem = '/ifs/work/solitlab/huw/program/RSEM_tutorial/ref/GRCm38/GRCm38'