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Old 08-21-2012, 06:32 AM   #1
alexischr
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Default Seurat - Analysis tool for tumor/normal DNA and RNA seq

Hello everyone,

I'd like to present Seurat, an analysis tool that we developed here at TGen. It detects somatic mutation (SNVs, indels, structural variance) and allelic imbalance in paired tumor/normal genome and transcriptome data.

The code was made into a GATK module, so its use will probably be familiar to some. Input is indexed BAMs, and output is split into a VCF file for simple events and a tab-delimited text file for larger events.

The latest release (and documentation) is at https://sourceforge.net/projects/seurat/ and we'd appreciate feedback, comments and suggestions! Right now the software is free from academic and research use.

Thanks!

-- Alexis Christoforides
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Old 06-06-2013, 05:09 AM   #2
nbahlis
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is is possible to run Seurat without RNAseq data?
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Old 06-06-2013, 10:54 PM   #3
Jon_Keats
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Great Job Alexis, first runs with the new version are coming off right now... Looks great as always
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Old 06-06-2013, 10:57 PM   #4
Jon_Keats
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Nizar, it will run on just the Tumor/normal DNA bam, RNA bam files are NOT required.
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Old 06-07-2013, 03:06 PM   #5
nbahlis
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thanks Jonathan, just started the analysis with Seurat, looks its gonna take FEW hours. I tweaked the script to add more memory to Java " java -Xmx2g -jar Seurat.jar ...". Without adding "-Xmx2g" I was getting a message "java heap OutOMemory".
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Old 10-31-2013, 11:16 AM   #6
agupta29
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Quote:
-refseq <refseq_file> Name of RefSeq transcript annotation file. If specified, gene-wide events can be detected, and SNVs/LOH events will be annotated with the gene name.
Can someone direct me to a source for the hg19, UCSC transcript annotation file. I generated one from the knownGene.txt file in iGenomes' hg19 package using genePredToGtf.

However, I keep getting the error:
Quote:
##### ERROR stack trace
java.lang.NumberFormatException: For input string: "."
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:481)
at java.lang.Integer.parseInt(Integer.java:527)
at org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec.decodeLoc(RefSeqCodec.java:72)
at org.broad.tribble.index.FeatureIterator.readNextFeature(IndexFactory.java:287)
at org.broad.tribble.index.FeatureIterator.<init>(IndexFactory.java:239)
at org.broad.tribble.index.IndexFactory.createIndex(IndexFactory.java:123)
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:361)
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:258)
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:199)
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:128)
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:145)
at org.broadinstitute.sting.gatk.walkers.tgen.Seurat.initialize(Seurat.java:106)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:48)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:246)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.5-32-g2761da9):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: For input string: "."
##### ERROR ------------------------------------------------------------------------------------------
I tried a few other sources for this file but the error persists.

Thanks
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