I am running GATK for snp analysis on my Ion S5 Samples
I am currently using reference file hg19 which i downloaded from gatk resource bundle
I am getting this error
any help is highly appreciable
INFO 11:37:24,559 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 11:37:24,907 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:37:24,908 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:37:24,909 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:37:24,911 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 11:37:25,012 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
WARN 11:37:25,012 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
INFO 11:37:25,014 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 11:37:54,935 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s
INFO 11:38:24,958 ProgressMeter - Starting 0.0 60.0 s 99.3 w 100.0% 60.0 s 0.0 s
INFO 11:38:54,959 ProgressMeter - Starting 0.0 90.0 s 148.9 w 100.0% 90.0 s 0.0 s
INFO 11:39:24,959 ProgressMeter - Starting 0.0 120.0 s 198.5 w 100.0% 120.0 s 0.0 s
INFO 11:39:54,961 ProgressMeter - Starting 0.0 2.5 m 248.1 w 100.0% 2.5 m 0.0 s
INFO 11:40:24,962 ProgressMeter - Starting 0.0 3.0 m 297.7 w 100.0% 3.0 m 0.0 s
INFO 11:40:54,963 ProgressMeter - Starting 0.0 3.5 m 347.3 w 100.0% 3.5 m 0.0 s
INFO 11:41:24,964 ProgressMeter - Starting 0.0 4.0 m 396.9 w 100.0% 4.0 m 0.0 s
INFO 11:41:54,965 ProgressMeter - Starting 0.0 4.5 m 446.5 w 100.0% 4.5 m 0.0 s
INFO 11:42:24,966 ProgressMeter - Starting 0.0 5.0 m 496.1 w 100.0% 5.0 m 0.0 s
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: 200
at org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase(ReferenceContext.java:179)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.getFilteredAndStratifiedContexts(UnifiedGenotypingEngine.java:482)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotypingEngine.java:218)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:375)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:147)
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:316)
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)