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We can make this file beautiful and searchable if this error is corrected: It looks like row 7 should actually have 1 column, instead of 2 in line 6.
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config.tsv
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executable file
·102 lines (102 loc) · 3.24 KB
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##########################
# #
#genearl annotation paths#
# #
##########################
#this is the dir that I put almost all the annotation files, so I can reuse this to refer to the dir
anno /home/ruping/shared/annotation/
#species, e.g., hg19, mm10, which is the prefix of many annotation files
species hg19
#chromosomes to be analyzed
chrs 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
#genome fasta file
GFASTA $anno/hg19.other/hg19.fasta
#Rscript bin
R R
RscriptBin Rscript
#java bin
java java
#size of chromosomes
chromosomeSize $anno/trupanno/$species/$species.chromosome_size.txt
####################
# #
#For read alignment#
# #
####################
#BWA bin
bwaBin bwa
#BWA mapping index
BWAINDEX $anno/hg19.other/hg19.bwa.index/hg19.fasta
#bowtieBin
bowtieBin bowtie2
#bowtie2 mapping index
BowtieINDEX $anno/trupanno/hg19/hg19.bowtie2_index/hg19/hg19
#blat database
blatDatabase $anno/trupanno/$species/$species.genome_UCSC.2bit
####################
# #
#for bam processing#
# #
####################
#java bin for gatk
gatkBin /srv/gsfs0/projects/curtis/ruping/tools/gatk/GenomeAnalysisTK.jar
#java bin for markduplicates
MarkDuplicatesBin /home/ruping/shared/tools/picard-tools/picard.jar
#samtools bin
samtoolsBin samtools
#bcftools bin
bcftoolsBin bcftools
#known indels for indel Realignment
KNOWNINDEL1 $anno/hg19.other/1000G_phase1.indels.b37.vcf
#known indels for indel Realignment
KNOWNINDEL2 $anno/hg19.other/Mills_and_1000G_gold_standard.indels.b37.vcf
####################
# #
#mutect snv calling#
# #
####################
#muTect bin
muTectBin /home/ruping/shared/tools/muTect/muTect-1.1.4.jar
#vcfSortBin
vcfSortBin vcf-sort
#mutect cosmic annotation vcf
muTectCOSMIC $anno/hg19.other/hg19_cosmic_v54_120711.nochr.vcf
#mutect dbSNP annotation vcf
muTectDBSNP $anno/hg19.other/dbsnp_132_b37.leftAligned.nochr.vcf
####################
# #
#strelka indel call#
# #
####################
#strelka Bin
strelkaBin /srv/gsfs0/projects/curtis/ruping/tools/strelka/strelka_workflow-1.0.14/bin/configureStrelkaWorkflow.pl
#strelka config file
strelkaConfig /srv/gsfs0/projects/curtis/ruping/tools/strelka/strelka_workflow-1.0.14/etc/strelka_config_bwa_default_wes.ini
####################
# #
#variant annotation#
# #
####################
#annovar bin dir
ANNOVARDIR /home/ruping/shared/tools/annovar.new/annovar/
#annovar annotation dir
ANNOVARDB $anno/annovardb/humandb.new/
#UCSC repeat masker file
repeatMasker $anno/trupanno/$species/$species.repeats_UCSC.gff
#UCSC self chain file
selfChain $anno/trupanno/$species/$species.SelfChain_UCSC.txt
############################
# #
#sequencing stats, TitanCNA#
# #
############################
#target region
targetRegion $anno/hg19.other/SureSelect_All_Exon_V4_hg19.bed.sorted.bed.w5
#genome bed 1kb
w1kBed $anno/hg19.other/hg19.w1k.bed
#targeted region for TitanCNA
targetRegionTitan $anno/hg19.other/SureSelect_All_Exon_V4_hg19.bed.sorted.bed
#gc wig for TitanCNA
gcWigTitan $anno/hg19.other/hg19.gc.wig
#map wig for TitanCNA
mapWigTitan $anno/hg19.other/hg19.map.wig