Hi,

I am running two separate reciprocal overlap (RO) analysis on ERDS variants and CNVnator variants. 

1. While running RO between two ERDS dataset, I was getting an error stating the 'REF' cannot be empty. So substituted the REF column with N. After running the script, I got the following error. 

INFO 07:31:51,493 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 07:31:51,495 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7.GS-r1941-0-gb493839, Compiled 2020/01/21 11:34:26
INFO 07:31:51,496 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 07:31:51,496 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 07:31:51,496 HelpFormatter - [Tue Jun 02 07:31:51 EDT 2020] Executing on Linux 3.10.0-862.9.1.el7.x86_64 amd64
INFO 07:31:51,496 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_201-b09
INFO 07:31:51,499 HelpFormatter - Program Args: -A ReciprocalOverlap -R /scratch/RESOURCES/hg19/human_g1k_v37.fasta -vcf /scratch/wgs/XKGP7WU/KEL8946.20190904/edited_7_0480_006.erds.vcf -comparisonFile /scratch/wgs/XKGP7WU/KEL8946.20190904/edited_7_0480_007.erds.vcf -O erds.FAM1_MU006_FAM1_MU007.ReciprocalOverlap.vcf -reciprocalOverlapRankBy FRACTION -writeReport true -reportDirectory reportdir -T SVVariantAnnotatorWalker
INFO 07:31:51,503 HelpFormatter - Executing as root@localhost.localdomain on Linux 3.10.0-862.9.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_201-b09.
INFO 07:31:51,503 HelpFormatter - Date/Time: 2020/06/02 07:31:51
INFO 07:31:51,503 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 07:31:51,503 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 07:31:51,514 02-Jun-2020 GenomeAnalysisEngine - Strictness is SILENT
INFO 07:31:51,627 02-Jun-2020 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 07:31:51,706 02-Jun-2020 GenomeAnalysisEngine - Preparing for traversal
INFO 07:31:51,711 02-Jun-2020 GenomeAnalysisEngine - Done preparing for traversal
INFO 07:31:51,711 02-Jun-2020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 07:31:51,712 02-Jun-2020 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 07:31:51,712 02-Jun-2020 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 07:31:51,712 02-Jun-2020 Walker - Initializing annotator framework ...
INFO 07:31:51,768 02-Jun-2020 Walker - Annotator framework initialization complete.
INFO 07:31:51,775 02-Jun-2020 Walker - Processing input file /scratch/wgs/XKGP7WU/KEL8946.20190904/edited_7_0480_006.erds.vcf ...
##### ERROR --
##### ERROR stack trace
htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: LineIteratorImpl(SynchronousLineReader), for input source: /scratch/wgs/XKGP7WU/KEL8946.20190904/edited_7_0480_006.erds.vcf
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:387)
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.<init>(TribbleIndexedFeatureReader.java:342)
at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:309)
at org.broadinstitute.sv.util.vcf.VCFReader.iterator(VCFReader.java:69)
at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.processVCFFile(SVVariantAnnotatorWalker.java:184)
at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.map(SVVariantAnnotatorWalker.java:134)
at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.map(SVVariantAnnotatorWalker.java:73)
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:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:145)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:95)
at org.broadinstitute.sv.main.SVAnnotator.main(SVAnnotator.java:92)
Caused by: java.lang.NumberFormatException: For input string: "N"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at htsjdk.variant.vcf.VCFUtils.parseVcfDouble(VCFUtils.java:262)
at htsjdk.variant.vcf.AbstractVCFCodec.parseQual(AbstractVCFCodec.java:620)
at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:422)
at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:384)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:328)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:48)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:70)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:37)
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:373)
... 16 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1941-0-gb493839):
##### 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 https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Error parsing line at byte position: LineIteratorImpl(SynchronousLineReader), for input source: /scratch/wgs/XKGP7WU/KEL8946.20190904/edited_7_0480_006.erds.vcf
##### ERROR ------------------------------------------------------------------------------------------

2. While running RO analysis between two CNVnator dataset, I get the output dat file and vcf file. While analyzing the dat file, I came across that some ID's in 'BESTHIT' , start position in 'BHSTART' aren't present in any of my input file. I don't know how that's possible.

For example, the highlighted ID 'CNVnator_dup_3' isn't present in any of my input file. 

Can you please let me know how to proceed?

Thanks!