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BreakTrans

Uncovering the genomic architecture of gene fusions

BreakTrans maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events and provide them mechanism/functional interpretation.

Web site
Reference

BreakTrans On Helix
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This example uses the same dataset described in the publication (User input in bold.)

[user@helix ~]$ module load BreakTrans

[user@helix ~]$ BreakTrans.pl \
    -g $BREAKTRANS_HOME/database/Human.Mar2006.RefSeqGenes.tab \
    -C $BREAKTRANS_HOME/database/Human.Mar2006.chainSelf.chr \
    $BREAKTRANS_HOME/testdata/SK-BR-3.dna.bd \
    $BREAKTRANS_HOME/testdata/SK-BR-3.rna.bd > SK-BR-3.drdb

[user@helix ~]$ cat SK-BR-3.drdb
#BreakTrans-0.0.6  /usr/local/apps/BreakTrans/0.0.6/testdata/SK-BR-3.dna.bd /usr/local/apps/BreakTrans/0.0.6/testdata/SK-BR-3.rna.bd
#Chr1	Pos1	Chr2	Pos2	Source	GeneFusion	SelfChainScore	GenomicAllele
3	4393009	3	37145643	BreakDancer	SUMF1>LRRFIP2	0	3:4338455-34|3:37158400-
3	4427552	3	37145643	BreakDancer	SUMF1>LRRFIP2	0	3:4338455-34|3:37158400-
5	139805747	5	141214187	BreakDancer	ANKHD1-EIF4EBP3>PCDH1	0	5:139807117+12|5:141217133-
8	119503847	8	121547840	BreakDancer	MTBP>SAMD12	0	8:121548224+38|8:119503735+0|8:119666167+2|8:119661057-
8	125620458	17	35315620	BreakDancer	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620458	17	35315169	BreakDancer	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620458	17	35319529	BreakDancer	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620458	17	35318707	BreakDancer	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620458	17	35315882	BreakDancer	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	79647680	17	35718963	BreakDancer	RARA>PKIA	0	17:35727917+45|8:79637984+
8	79673281	17	35718963	BreakDancer	RARA>PKIA	0	17:35727917+45|8:79637984+
8	81896406	8	124165759	BreakDancer	WDR67>ZNF704	0	8:81889478-16|8:81885125+0|8:81916434+18|8:124171162-0|8:124161970-23|8:124164299+,8:124171162+18|8:81916434-
14	99072104	14	98950023	TophatFusionPaper	CCDC85C>SETD3	0	14:99059254-7|14:98966917-
14	99072105	14	98950024	Defuse	CCDC85C>SETD3	0	14:99059254-7|14:98966917-
17	35719060	8	79647597	Tophat	RARA>PKIA	0	17:35727917+45|8:79637984+
17	35719061	8	79642268	Tophat	RARA>PKIA	0	17:35727917+45|8:79637984+
17	35719061	8	79673145	Tophat	RARA>PKIA	0	17:35727917+45|8:79637984+
17	35719061	8	79673145	TophatFusionPaper	RARA>PKIA	0	17:35727917+45|8:79637984+
17	35719064	8	79647601	Defuse	RARA>PKIA	0	17:35727917+45|8:79637984+
20	46797753	20	33678749	Defuse	PREX1>CPNE1	0	20:46795673-17|20:33925625-0|20:33923847-18|20:33679982-
3	4393012	3	37145642	TophatFusionPaper	SUMF1>LRRFIP2	0	3:4338455-34|3:37158400-
3	4393014	3	37145644	Defuse	SUMF1>LRRFIP2	0	3:4338455-34|3:37158400-
5	139805741	5	141214186	TophatFusionPaper	ANKHD1-EIF4EBP3>PCDH1	0	5:139807117+12|5:141217133-
5	139805744	5	141214185	Defuse	ANKHD1-EIF4EBP3>PCDH1	0	5:139807117+12|5:141217133-
8	119503797	8	121547851	Defuse	MTBP>SAMD12	0	8:121548224+38|8:119503735+0|8:119661057+2|8:119666167-0|8:119665498-47|8:119661057+0|8:119666167+2|8:119661057-
8	124165758	8	81896406	TophatFusionPaper	WDR67>ZNF704	0	8:124171162+18|8:81916434-
8	124165761	8	81896405	Defuse	WDR67>ZNF704	0	8:124171162+18|8:81916434-
8	125620346	17	35315760	Tophat	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620348	17	35319701	Tophat	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620350	17	35315764	Defuse	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620350	17	35319703	Defuse	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620443	17	35315760	Tophat	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620445	17	35316048	Tophat	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620445	17	35319701	Tophat	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620445	17	35319701	TophatFusionPaper	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620446	17	35316765	Tophat	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620447	17	35315764	Defuse	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620447	17	35316050	Defuse	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	125620447	17	35319703	Defuse	TATDN1>GSDMB	0	8:125618280-93|17:35321200-
8	79673148	17	35719064	Defuse	RARA>PKIA	0	17:35727917+45|8:79637984+

Running a single BreakTrans job on Biowulf
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Set up a batch script along the following lines:

#!/bin/bash
# file called myjob.bat

module load BreakTrans
cd /data/$USER
BreakTrans.pl \
    -g $BREAKTRANS_HOME/database/Human.Mar2006.RefSeqGenes.tab \
    -C $BREAKTRANS_HOME/database/Human.Mar2006.chainSelf.chr \
    $BREAKTRANS_HOME/testdata/SK-BR-3.dna.bd \
    $BREAKTRANS_HOME/testdata/SK-BR-3.rna.bd > SK-BR-3.drdb

Submit this job with:

[user@biowulf ~]$ sbatch myjob.bat

For more information on submitting jobs to slurm, see Job Submission in the Biowulf User Guide.

Running a swarm of BreakTrans jobs on Biowulf
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Sample swarm command file

# --------file myjobs.swarm----------
BreakTrans.pl genome-breakpoints1.dna.bd gene-fusion1.dna.bd > output1.drdb
BreakTrans.pl genome-breakpoints2.dna.bd gene-fusion2.dna.bd > output2.drdb
BreakTrans.pl genome-breakpoints3.dna.bd gene-fusion3.dna.bd > output3.drdb
....
BreakTrans.pl genome-breakpointsN.dna.bd gene-fusionN.dna.bd > outputN.drdb
# -----------------------------------

Submit this set of runs to the batch system by typing

[user@biowulf ~]$ swarm --module BreakTrans -f myjobs.swarm

For details on using swarm see Swarm on Biowulf.

Documentation
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