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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:
But I get the following error:
The dbsnp_131_hg19 rod file I am using looks like:
Any help to solve this error?
Many thanks,
David
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
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)
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
Many thanks,
David