Junction Location Identifier (JuLI)

J Mol Diagn. 2020 Mar;22(3):304-318

Update JuLI

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.

Installing JuLI

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

Input of JuLI

Sorted BAM

Running JuLI

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.

Output of JuLI

• 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)

Interpretation of JuLI

• 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

Test JuLI

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')