Seurat - Analysis tool for tumor/normal DNA and RNA seq

[alexischr]

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

[nbahlis]

is is possible to run Seurat without RNAseq data?

[Jon_Keats]

Great Job Alexis, first runs with the new version are coming off right now... Looks great as always

[Jon_Keats]

Nizar, it will run on just the Tumor/normal DNA bam, RNA bam files are NOT required.

[nbahlis]

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".

[agupta29]

-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:

##### 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