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For input string "." error

I have done a CNV analysis with Delly and wanted select variants on the output Delly file. But I seem to get this error that I can't resolve. Can someone help me resolve this? I can't seem to do any GATK related analysis as I get the same error "java.lang.NumberFormatException: For input string: ".""

This is the complete error report...

ERROR stack trace

java.lang.NumberFormatException: For input string: "."
at sun.misc.FloatingDecimal.readJavaFormatString(
at java.lang.Double.parseDouble(
at htsjdk.variant.variantcontext.GenotypeLikelihoods.parseDeprecatedGLString(
at htsjdk.variant.variantcontext.GenotypeLikelihoods.fromGLField(
at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(
at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(
at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(
at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(
at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(
at htsjdk.variant.vcf.AbstractVCFCodec.decode(
at htsjdk.variant.vcf.AbstractVCFCodec.decode(
at htsjdk.tribble.AsciiFeatureCodec.decode(
at htsjdk.tribble.AsciiFeatureCodec.decode(
at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(
at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(
at htsjdk.tribble.index.IndexFactory$
at htsjdk.tribble.index.IndexFactory.createIndex(
at htsjdk.tribble.index.IndexFactory.createDynamicIndex(
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createIndexInMemory(
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.engine.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
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
ERROR MESSAGE: For input string: "."
ERROR ------------------------------------------------------------------------------------------


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