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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
File metadata and controls
executable file
·89 lines (89 loc) · 3.04 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 /srv/gsfs0/projects/curtis/ruping/annotation/trupanno/
#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 $anno/$species/$species.bowtie2_index/$species/$species.fa
#Rscript bin
RscriptBin /srv/gsfs0/projects/curtis/ruping/tools/R/bin/Rscript
#size of chromosomes
chromosomeSize $anno/$species/$species.chromosome_size.txt
####################
# #
#For read alignment#
# #
####################
#bowtieBin
bowtieBin bowtie2
#bowtie2 mapping index
Bowtie2INDEX $anno/$species/$species.bowtie2_index/$species/$species
#GMAP index
gmap_index $anno/$species/$species.gmap_index/
#GMAP splice site
gmap_splicesites $anno/$species/$species.gmap_index/$species/$species.splicesites.iit
#STAR index
STAR_INDEX $anno/$species/$species.star/
#blat database
blatDatabase $anno/$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 /srv/gs1/software/picard-tools/1.111/MarkDuplicates.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
####################
# #
#gene annotation#
# #
####################
#gene annotation
gene_annotation $anno/$species/$species.transcripts_Ensembl.gff
#gene annotation gtf
gene_annotation_gtf $anno/$species/$species.transcripts_Ensembl.gtf
#ensembl gene bed
ensembl_gene_bed $anno/$species/$species.genes_Ensembl.bed12
#ensembl_gene_len
ensembl_gene_len $anno/$species/$species.genelength.ensembl
#gencode genemap
gencode_genemap $anno/$species/$species.gencode/gencode.v14.genemap
#gencode_gene_bed
gencode_gene_bed $anno/$species/$species.gencode/gencode.v14.annotation.gene.bed12
#ensembl_genemap
ensembl_genemap $anno/$species/$species.biomart.txt
#refseq_gene
refseq_gene $anno/$species/$species.genes_RefSeq.bed12
#refseq_gene_gtf
refseq_gene_gtf $anno/$species/$species.refGene.gtf
####################
# #
#variant annotation#
# #
####################
#annovar bin dir
ANNOVARDIR /srv/gsfs0/projects/curtis/ruping/tools/annovar.new/annovar/
#annovar annotation dir
ANNOVARDB $anno/annovardb/humandb.new/
#UCSC repeat masker file
repeatMasker $anno/$species/$species.repeats_UCSC.gff
#UCSC self chain file
selfChain $anno/$species/$species.SelfChain_UCSC.txt
#vcf header
vcfheader $anno/$species/$species.vcfheader_forAnnovar