SVGenotyper Error: Insert Size Record

dantakidantaki La JollaMember

I have a list of SVs from the 1kg phase3 VCF file that has been reduced to CNVs. The VCF file has the first 8 columns of the original from 1kg.

I want to use 27 high coverage genomes from 1kg on my local drive. I have a list with the full directory of these bam files.

The error message I'm getting is telling me I need an "insert size record". But looking at the documentation for genome STRIP and SVGenotyper (ctrl-F insert) returns nothing. The cookbook example executes without error

`##### ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.RuntimeException: No insert size data for record: H7AGFADXX131213:2:2111:16290:18730
at org.broadinstitute.sv.genotyping.ReadPairMapper.processSingleRead(ReadPairMapper.java:231)
at org.broadinstitute.sv.genotyping.ReadPairMapper.searchWindow(ReadPairMapper.java:193)
at org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:175)
at org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:106)
at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.getReadPairs(GenotypingReadPairModule.java:201)
at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeSample(GenotypingReadPairModule.java:94)
at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:64)
at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:39)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:141)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:106)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.processVCFFile(SVGenotyperWalker.java:282)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:226)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:59)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:106)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: No insert size data for record: H7AGFADXX131213:2:2111:16290:18730
ERROR ------------------------------------------------------------------------------------------`
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