software that finding gene fusions on exome sequencing?

libiyagirl · 07-19-2011, 08:30 AM

Hi all,

I'm thinking using exome sequencing data to look at gene fusions or larger indels. Does anyone know which software is good for this? I know it's going to be difficult because most breakpoints are in introns. Any suggesion?

Thank you!

ymc · 08-04-2013, 12:44 AM

FusionMap can also work on genomic DNA sequences. I am not sure if it works for exome-seq.

This paper seems to be able to find fusion genes from exome-seq. I wonder what software they use to do that

http://www.ncbi.nlm.nih.gov/pubmed/23313954

stianlagstad · 04-08-2016, 06:29 AM

Quote:

Originally Posted by ymc

FusionMap can also work on genomic DNA sequences. I am not sure if it works for exome-seq.

This paper seems to be able to find fusion genes from exome-seq. I wonder what software they use to do that

http://www.ncbi.nlm.nih.gov/pubmed/23313954

Sorry to bring back such an old post, but I went through a little hassle to figure it out and I think it might be useful for others:

They used dRanger (not publicly available) and Breakpointer.

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07-19-2011, 08:30 AM	#1
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	software that finding gene fusions on exome sequencing? Hi all, I'm thinking using exome sequencing data to look at gene fusions or larger indels. Does anyone know which software is good for this? I know it's going to be difficult because most breakpoints are in introns. Any suggesion? Thank you!

08-04-2013, 12:44 AM	#2
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	FusionMap can also work on genomic DNA sequences. I am not sure if it works for exome-seq. This paper seems to be able to find fusion genes from exome-seq. I wonder what software they use to do that http://www.ncbi.nlm.nih.gov/pubmed/23313954