Hi,
after running 5 exomes with GATK-v3.3 and HaplotypeCaller, I encountered a very low titv ration in my samples (~2.1) as VaraintEval report indicated. I tried running varaint filtration in these samples but I didn't see any imporvement in titv ratio nor any filtering done. therefore I filtered these with bcftools, after which the titv ratio improved to 2.5. Then when I tried running GenotypeGVCFs on these samples filtered with bcftools, I encountered the following error:
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.ClassCastException: java.lang.Integer cannot be cast to java.lang.Double
at java.lang.Double.compareTo(Double.java:49)
at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:290)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:157)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:146)
at java.util.Arrays.sort(Arrays.java:472)
at java.util.Collections.sort(Collections.java:155)
at org.broadinstitute.gatk.utils.MathUtils.median(MathUtils.java:999)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.combineAnnotationValues(ReferenceConfidenceVariantContextMerger.java:73)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:158)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:202)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:121)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
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:310)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
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.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2014-11-17-g58cfab1):
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: java.lang.Integer cannot be cast to java.lang.Double
ERROR ------------------------------------------------------------------------------------------
any advice on solving this incident will be much appreciated
Victoria