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Old 08-17-2011, 09:26 AM   #1
david.tamborero
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Location: spain

Join Date: Feb 2011
Posts: 60
Default Error during GATK SomaticIndelDetector

Hi,

I'm currently working in a pipeline to assess somatic mutations (SNPs/indels) so I am checking the SomaticIndelDetector tool from GenomeAnalysisTK-1.1-25.

The command I use is the following:

Code:
java -jar /path/to/GenomeAnalysisTK.jar -T SomaticIndelDetector \
        -R my.reference.fasta \
     -I:normal normal.sequencing.data.bam \
     -I:tumor tumor.sequencing.data.bam \
     -verbose my.detailed.output.txt \
     -o my.output.vcf \
     --refseq /path/to/refseq.rod
But I get the following error:

Code:
##### ERROR stack trace 
java.lang.NumberFormatException: For input string: "rs56289060"
	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
	at java.lang.Integer.parseInt(Integer.java:449)
	at java.lang.Integer.parseInt(Integer.java:499)
	at org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec.decode(RefSeqCodec.java:56)
	at org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec.decode(RefSeqCodec.java:17)
	at org.broad.tribble.source.BasicFeatureSource$IteratorImpl.readNextRecord(BasicFeatureSource.java:291)
	at org.broad.tribble.source.BasicFeatureSource$IteratorImpl.<init>(BasicFeatureSource.java:263)
	at org.broad.tribble.source.BasicFeatureSource.iterator(BasicFeatureSource.java:234)
	at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack.getIterator(RMDTrack.java:108)
	at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetectorWalker.initialize(SomaticIndelDetectorWalker.java:264)
	at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:48)
	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225)
	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:104)
	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:227)
	at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:89)
The dbsnp_131_hg19 rod file I am using looks like:

Code:
585	chr1	10433	10433	rs56289060	0	+	-	-	-/C	genomic	insertion	unknown	0	0	near-gene-5	between	1
585	chr1	10491	10492	rs55998931	0	+	C	C	C/T	genomic	single	unknown	0	0	near-gene-5	exact	1
585	chr1	10518	10519	rs62636508	0	+	G	G	C/G	genomic	single	unknown	0	0	near-gene-5	exact	1
Any help to solve this error?

Many thanks,
David
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gatk, indel calling, somatic mutations, somaticindeldetector

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