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

[Bob H. <han...@br...>]

Hi, Thomas,

The problem is that Genome STRiP internally uses the ZN tag to mean 
something else, and there's a safety check to make
sure this tag has not been set by some other application (or isn't being 
incorrectly set twice by Genome STRiP).
Changing the mapping quality threshold won't help, as the ZN attribute 
is applied before the mapping quality is checked.

Unfortunately, there are no good short term workarounds that I can think 
of.  The choices are:
a) remove the ZN tags
b) disable the use of read pairs in genotyping (change 
genotyping.modules in the config file to remove "pairs")

-Bob

On 12/13/11 11:59 AM, Thomas Zichner wrote:
> 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
>
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