VariantRecalibrator - java.lang.NumberFormatException: For input string: "."
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Hello, I am just trying VariantRecalibrator on my 4 samples:

java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R gatk.ucsc.mm10.fa -input UnifiedGenotyper.output.snps.raw.vcf -nt 14 -recalFile file_for_ApplyRecalibration.recal -tranchesFile file_for_ApplyRecalibration.tranches -resource:sanger,known=false,training=true,truth=true mgp.v2.snps.annot.reformat.vcf -resource:dbnsp,known=true,training=false,truth=false,prior=6.0 mm10_dbsnp.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff -mG 4 -percentBad 0.05

which starts running then gives me this error: INFO 08:26:57,741 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NumberFormatException: For input string: "." at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:481) at java.lang.Integer.valueOf(Integer.java:582) at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec.decodeInts(AbstractVCFCodec.java:680) at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:641) at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:92) at org.broadinstitute.sting.utils.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:130) at org.broadinstitute.sting.utils.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:120) at org.broadinstitute.sting.utils.variantcontext.GenotypesContext.iterator(GenotypesContext.java:461) at org.broadinstitute.sting.utils.variantcontext.VariantContext.getCalledChrCount(VariantContext.java:922) at org.broadinstitute.sting.utils.variantcontext.VariantContext.getCalledChrCount(VariantContext.java:908) at org.broadinstitute.sting.utils.variantcontext.VariantContext.isMonomorphicInSamples(VariantContext.java:937) at org.broadinstitute.sting.utils.variantcontext.VariantContext.isPolymorphicInSamples(VariantContext.java:948) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantDataManager.isValidVariant(VariantDataManager.java:278) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantDataManager.parseTrainingSets(VariantDataManager.java:263) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.map(VariantRecalibrator.java:259) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.map(VariantRecalibrator.java:107) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23) at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:73) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:722)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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: For input string: "."
ERROR ------------------------------------------------------------------------------------------

I've used all three VCFs in other GATK tools without issues. Any help greatly appreciated!, many thanks, Lavinia.


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