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Error using VariantAnnotator -A PossibleDeNovo
I am trying too annotate novel variants. I have a VCF file containing a single trio family.
I have run CalculateGenotypePosteriors on my file with no problems. I ran this with GATK4. I tried to run VariantAnnotator but kept getting errors that my ped file was incorrect .. which i believe is a bug following other discussions on the GATK forum. A workaround it seems is to perform VariantAnnotator using GATK3
I installed GATK3.8 and ran the following commands
gatk3 -T VariantAnnotator -V Fin_Fam4.vcf.gz -o Fin_Fam4.denovo.vcf.gz -A PossibleDeNovo -R $Genome --pedigree Fin_Fam4.ped
I got the following error and cannot make heads or tails of it nor can i find an example similar to this on the GATK forums. Would it be possible to take a look and advise?
ERROR stack trace
java.lang.IndexOutOfBoundsException: Index: 1, Size: 1 at java.util.ArrayList.rangeCheck(ArrayList.java:657) at java.util.ArrayList.get(ArrayList.java:433) at htsjdk.variant.variantcontext.VariantContext.getAlternateAllele(VariantContext.java:879) at org.broadinstitute.gatk.tools.walkers.annotator.PossibleDeNovo.annotate(PossibleDeNovo.java:164) at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:230) at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:212) at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:355) at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:112) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$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:98) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123) 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.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)