2019.12 V0.1.6: changed to also handle with NCBI style chromosome names (1,2..X,Y).
2020.10 V0.1.6.1: changed the errors from compatibility of data.table library.
2021.11 V0.1.6.2: fixed the bugs at merging bed files.
download https://github.com/sgilab/JuLI/raw/master/JuLI-v0.1.6.2.zip
unzip JuLI-vX.X.X.zip (type the downloaded version)
Open R (>= 3.3.1)
install.packages('devtools') # install library for installation
library(devtools) # load library
setwd('/path/JuLI-vX.X.X') # set download path
install('julivX.X.X') # install JuLI
Sorted BAM
Open R (>= 3.3.1)
library(julivX.X.X)
*Function for call fusions
callfusion(CaseBam='/InputPath/Input.bam',
TestID='TestID',
OutputPath='/OutputPath',
Thread=integer,
Refgene='/path/JuLI-vX.X.X/references/refGene_hg19.txt',
Gap='/path/JuLI-vX.X.X/references/gap_hg19.txt',
Reference='/path/hg19.fa')
[Options]
CaseBam: Path of case bam. If you want joint call from multiple bams, insert path of bams separated by comma (ex:CaseBam='/path/input1.bam,/path/input2.bam ...').
ControlBam: Path of control bam.
TestID: Name of sample. Default is a CaseBam name. If you want joint call, insert names separated by comma (ex:TestID='name1,name2 ...').
OutputPath: Path of output. Default is a path of case bam.
Thread: Thread number for parallel processing. Default is one thread.
ControlPanel: Path of control panel. The panel is generated by JuLI's 'controlpanel' function.
TargetBed: Path of target region file with BED format.
Refgene: Path of gene information file from UCSC database. It is uploaded to JuLI's github.
Gap: Path of gap information file from UCSC database. It is uploaded to JuLI's github.
Reference: Path of reference fasta file.
AnalysisType: Alignment type for analysis. Default is 'DP'. DP; discordant and proper pair, D; discordant pair only, P; proper pair only.
AnalysisUnit: Analysis unit of each processing. Default is 1000.
MinMappingQuality: Minimum mapping quality of analysis. Default is 0.
SplitCutoff: Cutoff of split reads. Default is two.
DiscordantCutoff: Cutoff of discordant reads. Default is three.
NucDiv: Use of nucleotide diversity filter. Default is TRUE.
SplitRatio: Split ratio cutoff of pairwise alignment. Default is 0.7.
MatchBase: Sequence length cutoff of pairwise alignment. Default is 10bp.
Log: Log file genereation. Default is FALSE.
*Function for annotation fusions
annofusion(Output='/OutputPath/TestID.txt',
Refgene='/path/JuLI-vX.X.X/references/Refgene_hg19.txt',
Cosmic='/path/JuLI-vX.X.X/references/CosmicFusionExport_V76.tsv',
Pfam='/path/JuLI-vX.X.X/references/Pfam-A.full.human',
Uniprot='/path/JuLI-vX.X.X/references/HGNC_GeneName_UniProtID_160524.txt')
[Options]
Output: Path of callfusion output.
Refgene: Path of gene information file from UCSC database. It is uploaded to JuLI's github.
Cosmic: Path of cosmic data file. It is uploaded to JuLI's github.
Pfam: Path of Pfam data file. It is uploaded to JuLI's github.
Uniprot: Path of Uniprot data file. It is uploaded to JuLI's github.
*Function for generation of control panel
controlpanel(ControlBams=c('/path/control1.bam,/path/control2.bam ...'),
ID='ID',
OutputPath='/OutputPath',
Thread=integer)
[Options]
ControlBams: Path of control bams separated by comma.
ID: Name of control panel.
OutputPath: Path of output.
Thread: Thread number for parallel processing. Default is one thread.
-
TestID.txt: raw output
-
TestID.annotated.txt: annotated output (strand specific event, flanking gene, frame, and cosmic)
-
TestID.annotated.gene.pdf: visualized gene-gene events with domain information
-
TestID.BamStat.txt: statistics of case bam
-
TestID.log: calling log (option)
-
chrA,B: reference sequence names of each breaks
-
OriA,B: fusion orientation of breaks of each breaks
0: 5 prime end of positive reference strand
1: 3 prime end of positive reference strand
-
DisA,B: discordant reads count supporting each breaks
-
SplitA,B: split reads count supporting each breaks
-
Event: rearrangement type (e.g. deletion, inversion, tandem, interchromosomal_translocation)
-
GeneA,B: gene names of each breaks
-
StrGeneA,B: strand of each genes
-
Direction: fusion direction
-
Frame: prediction of reading frame status of chimeric transcripts
Inframe: no frame change
Outframe: frame chage
Possible Outframe/inframe: frame prediction when breaks in exonic region
-
Cosmic: frequency of fusion events according cancer types
Open R (>= 3.3.1)
library(julivX.X.X)
callfusion(CaseBam='/path/JuLI-master/test/JuLI_test.bam',
TestID='JuLI_test',
OutputPath='/path/JuLI-master/test',
Thread=1,
Refgene='/path/JuLI-master/references/refGene_hg19.txt',
Gap='/path/JuLI-master/references/gap_hg19.txt',
Reference='/path/hg19.fa')
annofusion(Output='/path/JuLI-master/test/JuLI_test.txt',
Refgene='/path/JuLI-master/references/refGene_hg19.txt',
Cosmic='/path/JuLI-master/references/CosmicFusionExport_V76.tsv',
Pfam='/path/JuLI-master/references/Pfam-A.full.human',
Uniprot='/path/JuLI-master/references/HGNC_GeneName_UniProtID_160524.txt')