I am getting the error message below when genotyping a list of deletions (generated by another sv program) with GenomeSTRiP..
Are there any workarounds/solutions for this? I am getting this error messages at multiple sites.
The site in the vcf file starts with this....
1 28026606 rs764989478 CTTTT CT,C
INFO 21:07:28,727 SVGenotyper - Genotyping site: CNP rs763157369 NA 1 10450561 10450560 10450568 10450567
WARN 21:07:28,728 VariantJunctionGenerator - rs763157369_1: trimming 1/0 matching bases from junction
WARN 21:07:28,728 VariantJunctionGenerator - rs763157369_1: detected VNTR event of length 6: TTTTTT
WARN 21:07:28,728 VariantJunctionGenerator - rs763157369_2: detected VNTR event of length 7: TTTTTTT
INFO 21:07:28,728 SVGenotyper - GenotypingDepthModule processing site rs763157369 ...
Error: Exception processing cnp: Cannot handle multiple junction records: rs763157369
CNP: rs763157369 1:10450561-10450567
INFO 21:07:29,146 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.RuntimeException: Cannot handle multiple junction records: rs763157369
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getRefDepthInterval(GenotypingDepthModule.java:1179)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getRefDepthIntervals(GenotypingDepthModule.java:1152)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:227)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getReadCounts(GenotypingDepthModule.java:220)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getCnpReadCounts(GenotypingDepthModule.java:207)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:135)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:55)
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:268)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:214)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:56)
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:125)
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:79)
at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
