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Thread | Thread Starter | Forum | Replies | Last Post |
Structural variations using Newbler mapper | Soni | Bioinformatics | 2 | 12-06-2011 10:58 PM |
finding structural variations without paired reads | mike.t | Bioinformatics | 3 | 05-05-2011 11:23 AM |
inGAP-sv: a new tool to identify and visualize structural variations | biofqzhao | Bioinformatics | 0 | 02-20-2011 09:22 PM |
Structural Variations | sparks | Bioinformatics | 0 | 10-30-2008 03:16 PM |
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#1 |
Senior Member
Location: Palo Alto Join Date: Apr 2009
Posts: 213
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I would like to announce the release of Breakway, a program for identifying structural variations in genomic data!
http://breakway.sourceforge.net Breakway is a suite of programs (written in PERL) that take aligned genomic data and report structural variation breakpoints. Features include:
I've made Breakway so that it will be compatible with pipelines as well.There is the potential for Breakway to be plugged into your genome analysis pipeline to automatically generate a Breakway report. Development of Breakway started during analysis of the U87MG whole genome sequence and continued to mature throughout analysis of subsequent genome sequencing projects in the Stanley F. Nelson Lab at UCLA. Since that first project, Breakway has become significantly more powerful, and I feel has evolved (through concerted effort!) into something that the community would benefit from. I hope that Breakway can help others easily identify structural variation breakpoints in their genomic data. Please try it out! Last edited by Michael.James.Clark; 04-28-2010 at 10:39 AM. |
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#2 |
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Location: Boston area Join Date: Nov 2007
Posts: 747
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Note, the URL should be http://breakway.sourceforge.net
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#3 |
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Location: Palo Alto Join Date: Apr 2009
Posts: 213
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Oh, thanks! Serves me right for posting at 3:30AM right after I finished setting up the webpage.
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#4 |
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Location: Phoenix, AZ Join Date: Mar 2010
Posts: 279
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Nice looking application, do you think it can be used on mRNA-seq and exon capture datasets or just in whole genome sequencing?
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#5 |
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Location: Rockville Join Date: May 2009
Posts: 40
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I 'd like to try breakway, but before that it needs both bfast and DNAA in the path. when I install DNAA, I meet some problems. would you help me to fix it .
the error shows like this. $ make make all-recursive make[1]: Entering directory `/gs1/users/tangwei/dnaa-0.1.1/dnaa-0.1.1' Making all in dkbaseencoding make[2]: Entering directory `/gs1/users/tangwei/dnaa-0.1.1/dnaa-0.1.1/dkbaseencoding' if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -m64 -MT RGIndex.o -MD -MP -MF ".deps/RGIndex.Tpo" -c -o RGIndex.o `test -f '../bfast/bfast/RGIndex.c' || echo './'`../bfast/bfast/RGIndex.c; \ then mv -f ".deps/RGIndex.Tpo" ".deps/RGIndex.Po"; else rm -f ".deps/RGIndex.Tpo"; exit 1; fi ../bfast/bfast/RGIndex.c:20:26: error: RGIndexExons.h: No such file or directory make[2]: *** [RGIndex.o] Error 1 make[2]: Leaving directory `/gs1/users/tangwei/dnaa-0.1.1/dnaa-0.1.1/dkbaseencoding' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/gs1/users/tangwei/dnaa-0.1.1/dnaa-0.1.1' make: *** [all] Error 2 |
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#6 | |
Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Nils Last edited by nilshomer; 04-28-2010 at 09:51 PM. Reason: esl |
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#7 | |
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Location: Palo Alto Join Date: Apr 2009
Posts: 213
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Breakway functions by looking for clusters of aberrantly spaced paired reads, so the key is to have an appropriate reference genome for it to compare to. For exon capture, it should work with the normal reference genome just as well as it will with whole genomes. For RNAseq, and I'm not an expert so I welcome other suggestions, the transcriptome will probably be best used as the reference genome. |
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#8 | |
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Location: Palo Alto Join Date: Apr 2009
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townway, I just successfully installed DNAA from the current tarball on Sourceforge without any problems following the directions in the INSTALL file, so just try again and hopefully it'll work for you. |
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#9 |
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Location: Brisbane Join Date: Jan 2010
Posts: 8
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Does this work with mate pair data generated by the SOLiD platform. All I see in the manual are references to Paired End data, and the DNAA manual seems a little sparse on handling mate pair data too.
cheers |
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#10 |
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Location: Brisbane Join Date: Jan 2010
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sorry, i'm the idiot. just found it after a closer look
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#11 |
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Location: Palo Alto Join Date: Apr 2009
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Breakway should work with any paired data--paired-end or mate pair or even split long reads.
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#12 |
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Location: Palo Alto Join Date: Apr 2009
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Hi all,
A significant bug fix was just implemented such that breakway.run.pl will now function properly. Please update to Breakway 0.5.1! Please let me know if you find any more! MJ
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Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] Projects: U87MG whole genome sequence [Website] [Paper] Last edited by Michael.James.Clark; 05-05-2010 at 12:27 PM. |
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#13 |
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Location: Palo Alto Join Date: Apr 2009
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A request was made for a filtering script that allows one to use another Breakway file in order to cross-check the Breakway file being created for events present in both. This is particularly useful for two things (and maybe more):
1) Comparing a tumor with its germline genome when both have been aligned to the same reference. This is useful because the germline will often contain variants from the reference, as the reference is unrelated. The expectation is that since the tumor is derived from the germline, we expect the tumor to contain these unless there is a mutation. It should allow one to identify tumor-specific mutations. 2) Removing native events that are detected in the reference from the genome in question. This is because some structural events can be detected in the reference (for example, segmental duplications) and therefore may be worth marking in the sequenced genome. If you want to use this function, please go to the Breakway website and download Breakway 0.6. The script is in the scripts folder and is called "breakway.bwfilter.pl". You can also use the usual breakway.run.pl with the --bwfile option and it will work.
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Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] Projects: U87MG whole genome sequence [Website] [Paper] Last edited by Michael.James.Clark; 05-10-2010 at 11:24 PM. |
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#14 |
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Location: Brisbane Join Date: Jan 2010
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I'm getting errors on BAM files that have string flag fields instead of numerical flag fields.
ie, a read starting with this Code:
1155_400_505 pP1 chr1 2571 255 8M6D17M = is this a known bug, or somthing that can be worked around. cheers |
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#15 | |
Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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#16 |
Junior Member
Location: Brisbane Join Date: Jan 2010
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OK. I think that problem was simply the viewer telling me that read was a problem. I've got past that, but now get a
[main_samview] fail to get the reference name. Continue anyway. error, and nothing in the output. Does anyone know what that means? It happens during the sharpenedges part of the script. cheers |
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#17 |
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Location: sweden Join Date: Jul 2010
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Hello!
I'm trying to make structural variation calls from 1000 genomes data. I thought I might try breakway but ran into problems :/. When calculating PED values with the dnaa script dbampairedenddist I need to specify a certain range based on predicted PED from library generation. As far as I know the 1000 genomes bam-files take input from several different raw read files so how can I know which range to choose? Or does this make 1000 genomes data incompatible with breakway SV detection? Thank you very much! |
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#18 | |
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Location: Ann Arbor, MI Join Date: Oct 2008
Posts: 57
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#19 | |
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Location: Palo Alto Join Date: Apr 2009
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Sharpenedges uses samtools as part of its activity, and this is a samtools error. Make sure that you've properly indexed the BAM file, and that the file is in BAM format. If you still have a problem, please run samtools view and post an example read here for me to look at.
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Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] Projects: U87MG whole genome sequence [Website] [Paper] |
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#20 | |
Senior Member
Location: Palo Alto Join Date: Apr 2009
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If you have libraries with very different PEDs, it will have difficulty working correctly. You can isolate reads with very different PEDs from each other and run it independently on each one, then combine the results, though. This is what I have done. I'm not very familiar with 1000 genomes data, but if they use the read group flag in their BAM files with the library field clarifying which library specific RGs are sourced from, you can use that to isolate the reads. Sorry I can't be more help--Breakway was designed to function optimally on a sample-by-sample basis, not on a batch of samples.
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Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] Projects: U87MG whole genome sequence [Website] [Paper] |
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