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Old 10-31-2013, 11:16 AM   #6
agupta29
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Location: Madison

Join Date: Jan 2013
Posts: 5
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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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