Hi, I am using VariantAnnotator and, among other annotations, I would like to add also the allelic frequency of my SNPs in 1000G to the resulting annotated .vcf file.
I did this through the following command line
java -Xmx8g -jar /bio/GenomeAnalysisTK.jar -T VariantAnnotator -V ${1}/recalibratedSNPsINDELs.vcf -R /data/shared/noPAR.hg19_decoy.fa \
-resource:1000G /data/shared/sort.1000G_phase1.snps.high_confidence.hg19.vcf.gz \
-E 1000G.AF -E 1000G.pop --resourceAlleleConcordance \
-o ${1}.annotation1bis.vcf \
&> ${1}.annotation1bis.log
Nonetheless, the scripts stops after (successfully) annotating a few hundreds variants, with the following error message
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
at java.util.ArrayList.get(ArrayList.java:429)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateExpressions(VariantAnnotatorEngine.java:462)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:217)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:203)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:357)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:114)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$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:315)
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 3.5-0-g36282e4):
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: Index: 1, Size: 1
ERROR ------------------------------------------------------------------------------------------
I have found some similar errors in the forum but never the same as mine for VariantAnnotator..
Moreover, I have to say that when I remove the annotation of allelic frequencies in 1000G the script seems to work properly..what could be the reason for this?
I am looking forward to hearing from you.
Best,
Alessandro
(v3.5-0-g36282e4)