DNA パイプライン設定ファイルについて

パイプライン設定ファイルはGenomon実行時に読込まれるファイルです.各ツールのパスやパラメータを設定することができます.

注釈

HGCスパコンの場合,このファイルは /home/w3varann/genomon_pipeline-2.4.1/genomon_conf/ にあります.

exome解析用:dna_exome_genomon.cfg
wgs解析用:dna_wgs_genomon.cfg

ANNOVARの設定が必要ですので,まずは Quick Start DNA解析 から始めてください.

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#
# Genomon pipeline configuration file
#

[REFERENCE]
# prepared reference fasta file
ref_fasta                               = # the path to the GRCh37.fa
interval_list                           = # the path to the GRCh37_noScaffold_noDecoy.interval_list
genome_size                             = # the path to the bedtools-2.24.0/genomes/human.hg19.genome
gaptxt                                  = # the path to the gap.txt
bait_file                               = # the path to the refGene.coding.exon.151207.bed
simple_repeat_tabix_db                  = # the path to the simpleRepeat.bed.bgz
HGVD_2013_tabix_db                      = # the path to the DBexome20131010.bed.gz
HGVD_2016_tabix_db                      = # the path to the DBexome20160412.bed.gz
ExAC_tabix_db                           = # the path to the ExAC.bed.gz

[SOFTWARE]
# prepared tools
blat                                    = # the path to the blat_x86_64/blat
bwa                                     = # the path to the bwa-0.7.8/bwa
samtools                                = # the path to the samtools-1.2/samtools
bedtools                                = # the path to the bedtools-2.24.0/bin/bedtools
biobambam                               = # the path to the biobambam-0.0.191/bin
bamstats                                = # the path to the PCAP-core-dev.20150511/bin/bam_stats.pl
htslib                                  = # the path to the htslib-1.3
genomon_sv                              = # the path to the bin/GenomonSV
sv_utils                                = # the path to the bin/sv_utils
mutfilter                               = # the path to the bin/mutfilter
ebfilter                                = # the path to the bin/EBFilter
fisher                                  = # the path to the bin/fisher
mutanno                                 = # the path to the bin/mutanno
genomon_pa                              = # the path to the bin/genomon_pa
pa_plot                                 = # the path to the bin/pa_plot
mutil                                   = # the path to the bin/mutil

# annovar needs to be installed individually
annovar                                 = # the path to the annovar

[ENV]
PERL5LIB                                = # the path to the perl module
PYTHONHOME                              = # the path to the python home
PYTHONPATH                              = # the path to the python path
LD_LIBRARY_PATH                         = # the path to the python library


######################################################################
#
# 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
[qc_bamstats]
qsub_option = -l s_vmem=1G,mem_req=1G

[qc_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
samtools_params = -F 3072 -f 2

[qc_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]
pair_params = --min_depth 8 --base_quality 15 --min_variant_read 4 --min_allele_freq 0.02 --max_allele_freq 0.1 --fisher_value 0.1 --samtools_params "-q 20 -BQ0 -d 10000000 --ff UNMAP,SECONDARY,QCFAIL,DUP"
single_params = --min_depth 8 --base_quality 15 --min_variant_read 4 --min_allele_freq 0.02 --post_10_q 0.02 --samtools_params "-q 20 -BQ0 -d 10000000 --ff UNMAP,SECONDARY,QCFAIL,DUP"

[realignment_filter]
params = --score_difference 5 --window_size 200 --max_depth 5000 --exclude_sam_flags 3328

[indel_filter]
params = --search_length 40 --neighbor 5 --min_depth 8 --min_mismatch 100000 --af_thres 1 --samtools_params "-q 20 -BQ0 -d 10000000 --ff UNMAP,SECONDARY,QCFAIL,DUP"

[breakpoint_filter]
params = --max_depth 1000 --min_clip_size 20 --junc_num_thres 0 --mapq_thres 10 --exclude_sam_flags 3332

[eb_filter]
map_quality = 20
base_quality = 15
filter_flags = UNMAP,SECONDARY,QCFAIL,DUP

[annotation]
active_annovar_flag = False
annovar_buildver = hg19
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
annovar_database = /your_annovar/humandb
# Use of this HGVD database is subject to compliance with the terms of use.
# Please refere to the site below:
# http://www.genome.med.kyoto-u.ac.jp/SnpDB/about.html
active_HGVD_2013_flag = False
active_HGVD_2016_flag = False
# Use of this ExAC database is subject to compliance with the terms of use.
# Please refere to the site below:
# http://exac.broadinstitute.org/faq
active_ExAC_flag = False

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

[mutation_util]
pair_params = --fish_pval 1.0 --realign_pval 1.0 --eb_pval 4.0 --tcount 4 --ncount 2
single_params = --post10q 0.1 --r_post10q 0.1 --eb_pval 4.0 --count 4

##########
## Genomon SV

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

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

[sv_filt]
qsub_option = -l s_vmem=2G,mem_req=2G
params = --min_junc_num 2 --max_control_variant_read_pair 10 --min_overhang_size 30
annotation_dir = # the path to the GenomonSV-0.4.0beta/resource
sv_utils_params = --min_tumor_allele_freq 0.07 --max_control_variant_read_pair 1 --control_depth_thres 10 --inversion_size_thres 1000 --remove_simple_repeat
sv_utils_annotation_dir = # the path to the sv_utils-0.4.0beta/resource

##########
## Post Analysis
[pa_plot]
enable = True
include_unpair = True
include_unpanel = True
title = Genomon
remarks = Data used in this report were generated using below software.
software = genomon_pipeline:Genomon-Pipeline, genomon_sv:GenomonSV, sv_utils:sv_utils, fisher:GenomonFisher, mutfilter:GenomonMutationFilter, ebfilter:EBFilter, mutanno:mutanno, mutil:mutil

config_file = # the path to the paplot-0.2.8/paplot.cfg
qsub_option = -l s_vmem=2G,mem_req=2G

[post_analysis]
enable = True
config_file = # the path to the GenomonPostAnalysis-1.0.2/genomon_post_analysis.cfg
qsub_option = -l s_vmem=2G,mem_req=2G