[svtoolkit-help] SV Genotyping crashing because of ZN tag created by Novoalign

[Thomas Z. <tho...@em...>]

Hi,

I have about 50 bam files which were generated using Novoalign. Running 
the SV discovery on them works without any problems. However, if I try 
to run the SV genotyping, I get the following error message:


Error: Exception processing cnp: Tag ZN already set on read 
USI-EAS034_PE_FC30HJPAAXX:2:75:1436:50
CNP: del_664 chr2:359968-365840
INFO  17:25:39,596 GATKRunReport - Aggregating data for run report
##### ERROR 
------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Tag ZN already set on read 
USI-EAS034_PE_FC30HJPAAXX:2:75:1436:50
     at 
org.broadinstitute.sv.genotyping.ReadPairMapper.setRecordAttribute(ReadPairMapper.java:460)
     at 
org.broadinstitute.sv.genotyping.ReadPairMapper.processReadPair(ReadPairMapper.java:399)
     at 
org.broadinstitute.sv.genotyping.ReadPairMapper.processReadPairs(ReadPairMapper.java:327)
     at 
org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:176)
     at 
org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:100)
     at 
org.broadinstitute.sv.genotyping.GenotypingReadPairModule.getReadPairs(GenotypingReadPairModule.java:204)
     at 
org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeSample(GenotypingReadPairModule.java:78)
     at 
org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:63)
     at 
org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:122)
     at 
org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:94)
     at 
org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:183)
     at 
org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:53)
     at 
org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)
     at 
org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:19)
     at 
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:61)
     at 
org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
     at 
org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
     at 
org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
     at 
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
     at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
     at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)


For my Novoalign files, the ZN tag is set for all reads which have 
multiple mapping locations. In case of multiple mapping locations, the 
read is place randomly and the number of possible mapping locations is 
indicated in the ZN tag.

All of these reads have a very low mapping quality (usually 0), so I 
thought they should be anyway not considered by GenomeSTRiP.

Any help is very much appreciated.
Best regards
Thomas Zichner