forked from CompMeth/VSeq-Toolkit
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathconfig.test.txt
110 lines (83 loc) · 4.51 KB
/
config.test.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
################################ Config. File for VSeq-Toolkit ###############################
#Version 1.0 #Author: Saira Afzal #Last Updated: 22-Dec-2019
#NOTE: Each mode can be executed individually, or all 3 together or 2 & 3 together
#######################################################################################################
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@#
#General Parameters: Always set these parameters for executing any of the three MODES.
#Forward and reverse file of paired end WGS/TES data
file1= $VSeqToolkit/testDir/testData/testDataCombined.R1.fastq.gz
file2= $VSeqToolkit/testDir/testData/testDataCombined.R2.fastq.gz
#Output directory
outDir= $VSeqToolkit/testDir/testResultsCheck/
#Path to the bin scripts directory of VSeq-Toolkit
bin= $VSeqToolkit/scripts/
#Min. quality value and length after trimming, adapters forward and reverse file for trimming
qua=20
lenPer=50
adapter1=GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
#Path to the third-party tools required
trimmer= $VSeqToolkit/thirdPartyTools/skewer
aligner= $VSeqToolkit/thirdPartyTools/bwa
samtools= $VSeqToolkit/thirdPartyTools/samtools
#Mode default/sensitive
mode=default
#######################################################################################################
## MODE 1: Contaminants Distribution Analysis ##
######################################################@@@##############################################
#Contaminant distribution analysis true/false
contAna=true
#Path to the BWA reference index files. Before indexing concatenate all reference together in one file
combinedRef= $VSeqToolkit/testDir/testReferenceIndex/referenceTestCombined.fa
#Stringency/Specificity levels high/moderate/low/null (recommended medium/high for experimental data)
stringencyCont=low
#Threshold for specifying each read of the pair unique/multiple mapped
UMthresholdCont=0.95
#######################################################################################################
## MODE 2: Vector-Vector Fusion Analysis ##
#######################################################################################################
#Intra Vector fusion analysis true/false
vecVecFusion=true
#Path to the BWA reference index files of vector(s). For multiple vectors concatenate all together
vecRef= $VSeqToolkit/testDir/testReferenceIndex/vector1.fa
#Stringency/Specificity levels high/moderate/low/null (recommended medium/high for experimental data)
stringencyVec=low
#Threshold for specifying each read of the pair unique/multiple mapped
UMthresholdVec=0.95
#Minimum span of each vector region
minMapSpanVec=20
#Maximum unmapped bases between fusion regions
distVecVec=10
#Maximum overlapping bases between fusion regions
opVecVec=5
#Minimum identity of fusion regions
idenVecVec=95
#######################################################################################################
## MODE 3: Vector-Host Fusion Analysis ##
#######################################################################################################
#Integartion sites analysis True/False
vecGenIS=true
#Path to the BWA reference index files of vector(s). For multiple vectors concatenate all together
vecRef= $VSeqToolkit/testDir/testReferenceIndex/vector1.fa
#Provide index file after concatenating reference genome and vector(s)
vecGenRef= $VSeqToolkit/testDir/testReferenceIndex/hg38chr22Vector1.fa
#Stringency/Specificity levels high/moderate/low/null (recommended medium/high for experimental data)
stringencyVecGen=low
#Threshold for specifying a specific read as unique or multiple mapped
UMthresholdVecGen=0.95
#Minimum span of vector and genome regions
minMapSpanVecGen=20
#Maximum unmapped bases between fusion regions
distVecGen=10
#Maximum overlapping base pairs between vector and genome fusion regions
opVecGen=5
#Minimum identity of fusion regions of vector and genome
idenVecGen=95
#Range for position clustering on genomic fusion/insertion sites
clusterRange=3
#Path to the annotation information table - Refseq
annoTable= $VSeqToolkit/testDir/testReferenceIndex/refSeqUCSCTablehg38.txt
#Path to bedtools
bedtools= $VSeqToolkit/thirdPartyTools/bedtools
#######################################################################################################
#######################################################################################################