Configファイルについて

sample.cfg

入力ファイルの設定や、tumor, normalのサンプルのペア情報を記載します
くわしい使い方は Sample_confの書き方 に書かれています.

genomon.cfg

使用するソフトウェアやデータベースを管理しているファイルです。
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#
# Genomon pipeline configuration file
#

[REFERENCE]
# prepared reference fasta file
ref_fasta                               = /home/w3varann/genomon_pipeline-2.0.2/database/GRCh37/GRCh37.fa
genome_size                             = /home/w3varann/genomon_pipeline-2.0.2/database/GRCh37/GRCh37.fa.chrom.sizes
interval_list                           = /home/w3varann/genomon_pipeline-2.0.2/database/GRCh37/GRCh37_noScaffold_noDecoy.interval_list
star_genome                             = /home/w3varann/genomon_pipeline-2.0.2/database/GRCh37.STAR-STAR_2.4.0k
hg19_genome                             = /home/w3varann/genomon_pipeline-2.0.2/tools/bedtools-2.24.0/genomes/human.hg19.genome
gaptxt                                  = /home/w3varann/genomon_pipeline-2.0.2/database/hg19.fa/gap.txt
bait_file                               = /home/w3varann/genomon_pipeline-2.0.2/database/bait/refGene.coding.exon.151207.bed
simple_repeat_tabix_db                  = /home/w3varann/genomon_pipeline-2.0.2/database/tabix/simpleRepeat.bed.bgz
HGVD_tabix_db                           = /home/w3varann/genomon_pipeline-2.0.2/database/tabix/DBexome20131010.bed.gz

[SOFTWARE]
# prepared tools
python                                  = /usr/local/package/python2.7/current/bin/python
R                                       = /usr/local/package/r/current3_gcc/bin/R
blat                                    = /home/w3varann/genomon_pipeline-2.0.2/tools/blat_x86_64/blat
bwa                                     = /home/w3varann/genomon_pipeline-2.0.2/tools/bwa-0.7.8/bwa
samtools                                = /home/w3varann/genomon_pipeline-2.0.2/tools/samtools-1.2/samtools
bedtools                                = /home/w3varann/genomon_pipeline-2.0.2/tools/bedtools-2.24.0/bin/bedtools
biobambam                               = /home/w3varann/genomon_pipeline-2.0.2/tools/biobambam-0.0.191/bin
PCAP                                    = /home/w3varann/genomon_pipeline-2.0.2/tools/PCAP-core-dev.20150511
tophat2                                 = /home/w3varann/genomon_pipeline-2.0.2/tools/tophat-2.0.14.Linux_x86_64/tophat2
STAR                                    = /home/w3varann/genomon_pipeline-2.0.2/tools/STAR-STAR_2.4.0k/bin/Linux_x86_64/STAR
STAR-Fusion                             = /home/w3varann/genomon_pipeline-2.0.2/tools/STAR-Fusion-master/STAR-Fusion
genomon_sv                              = /home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/bin/GenomonSV
fusionfusion                            = /home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/bin/fusionfusion
mutfilter                               = /home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/bin/mutfilter
ebfilter                                = /home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/bin/EBFilter
fisher                                  = /home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/bin/fisher
mutanno                                 = /home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/bin/mutanno


# annovar needs to be installed individually
annovar                                 = /home/your_directory

[ENV]
# biobambam needs libmaus library. libmaus_PATH is going to be added in LD_LIBRARY_PATH.
libmaus_PATH                            = /home/w3varann/tools/libmaus/lib
# drmaa needs libdrmaa library. drmaa_PATH is goint to be set in DRMAA_LIBRARY_PATH.
drmaa_PATH                              = /geadmin/N1GE/lib/lx-amd64/libdrmaa.so.1.0
# STAR-Fusion needs to set perl lib path.
PERL5LIB                                = /home/w3varann/.local/lib/perl/lib:/home/w3varann/.local/lib/perl/lib/perl5:/home/w3varann/.local/lib/perl/lib/perl5/x86_64-linux-thread-multi

R_LIBS                                  = /home/w3varann/.R

PYTHONHOME                              = /usr/local/package/python2.7/current
PYTHONPATH                              = /home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/lib/python

# Add LD_LIBRARY_PATH to the current LD_LIBRARY_PATH
#add_LD_LIBRARY_PATH                        = /usr/local/package/python2.7/current/lib:/home/w3varann/.local/lib

# Change LD_LIBRARY_PATH to the following LD_LIBRARY_PATH
LD_LIBRARY_PATH                         = /usr/local/package/python2.7/current/lib:/home/w3varann/genomon_pipeline-2.0.2/python2.7-packages/lib

dna_task_param.cfg

DNAパイプライン実行時に使用されるファイルです。
各ツールオプションのパラメータを設定することができます。
またパイプラインの各Taskのqsubで使用するメモリ量を設定できます。
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######################################################################
#
# Analysis parameters
#
#   If not defined, default values are going to be used in the pipeline.
#

##########
# parameters for bam2fastq
[bam2fastq]
qsub_option = -l s_vmem=1G,mem_req=1G

##########
# parameters for split fastq
[split_fastq]
qsub_option = -l s_vmem=1G,mem_req=1G
split_fastq_line_number = 40000000
fastq_filter = False

##########
# parameters for bwa_mem
[bwa_mem]
qsub_option = -l s_vmem=10.6G,mem_req=10.6G
bwa_params = -T 0

##########
## BAM markduplicates
[markduplicates]
qsub_option = -l s_vmem=10.6G,mem_req=10.6G
java_memory = 10.6G

##########
# BAM file statistics
[bam_stats]
qsub_option = -l s_vmem=1G,mem_req=1G

[coverage]
qsub_option = -l s_vmem=1G,mem_req=1G
coverage    = 2,10,20,30,40,50,100
wgs_flag = False
wgs_incl_bed_width = 1000000
wgs_i_bed_lines = 10000
wgs_i_bed_width = 100

[merge]
qsub_option = -l s_vmem=1G,mem_req=1G

###########
# mutation call
[mutation_call]
qsub_option = -l s_vmem=5.3G,mem_req=5.3G

[fisher_mutation_call]
min_depth = 8
map_quality = 20
base_quality = 15
disease_min_allele_frequency = 0.02
control_max_allele_frequency = 0.1
fisher_thres_hold = 0.1
post_10_q = 0.02

[realignment_filter]
disease_min_mismatch=0
control_max_mismatch=100000
score_diff=5
window_size=200
max_depth=5000

[indel_filter]
search_length=40
neighbor=5
base_quality=20
min_depth=8
max_mismatch=100000
max_allele_freq=1

[breakpoint_filter]
max_depth=1000
min_clip_size=20
junc_num_thres=0
map_quality=10

[eb_filter]
map_quality = 20
base_quality = 15

[annotation]
active_annovar_flag = False
table_annovar_params = -buildver hg19 -remove --otherinfo -protocol refGene,cytoBand,genomicSuperDups,esp6500siv2_all,1000g2010nov_all,1000g2014oct_all,1000g2014oct_afr,1000g2014oct_eas,1000g2014oct_eur,snp131,snp138,snp131NonFlagged,snp138NonFlagged,cosmic68wgs,cosmic70,clinvar_20150629,ljb26_all -operation g,r,r,f,f,f,f,f,f,f,f,f,f,f,f,f,f
active_HGVD_flag = False

[mutation_merge]
qsub_option = -l s_vmem=2G,mem_req=2G

##########
## Genomon SV
[genomon_sv]
param_file = /home/w3varann/database/GenomonSV-0.1.0/param.yaml

[sv_parse]
qsub_option = -l s_vmem=2G,mem_req=2G

[sv_merge]
qsub_option = -l s_vmem=2G,mem_req=2G

[sv_filt]
qsub_option = -l s_vmem=2G,mem_req=2G

rna_task_param.cfg

RNAパイプライン実行時に使用されるファイルです。
使用方法としてはdna_task_param.cfgと同じ
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######################################################################
#
# Analysis parameters
#
#   If not defined, default values are going to be used in the pipeline.
#

##########
# parameters for bam2fastq
[bam2fastq]
qsub_option = -l ljob,s_vmem=1G,mem_req=1G

##########
# parameters for star alignment
[star_align]
qsub_option = -pe def_slot 6 -l s_vmem=5.3G,mem_req=5.3G
star_params = --runThreadN 6 --outSAMstrandField intronMotif --outSAMunmapped Within --alignMatesGapMax 500000 --alignIntronMax 500000 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --outSAMtype BAM Unsorted
samtools_sort_params = -@ 6 -m 3G

##########
# parameters for fusionfusion
[fusionfusion]
qsub_option = -l ljob,s_vmem=5.3G,mem_req=5.3G
param_file = /home/w3varann/database/fusionfusion_hg19/param.cfg