I'm running Mutect2 and Funcotator on WES samples on Terra (GATK v4.1.4.0), and am seeing the same reproducible "StringIndexOutOfBoundsException" error on ~6-7% of my samples. It looks like this was perhaps discussed on the old forum but I can't access those posts now. I'm running this using the Somatic-SNVs-Indels-GATK4 featured workspace, cloned on 12/31/2019. 

Here is the end of the error log for one example:

07:58:44.198 INFO Funcotator - Shutting down engine
[January 21, 2020 7:58:44 AM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 43.75 minutes.
Runtime.totalMemory()=1102577664
java.lang.StringIndexOutOfBoundsException: String index out of range: 412
at java.lang.String.substring(String.java:1963)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.initializeForDeletion(ProteinChangeInfo.java:192)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.<init>(ProteinChangeInfo.java:96)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.create(ProteinChangeInfo.java:371)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createSequenceComparison(GencodeFuncotationFactory.java:2003)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createCodingRegionFuncotationForProteinCodingFeature(GencodeFuncotationFactory.java:1193)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createExonFuncotation(GencodeFuncotationFactory.java:1044)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnSingleTranscript(GencodeFuncotationFactory.java:978)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:805)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:789)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.lambda$createGencodeFuncotationsByAllTranscripts$0(GencodeFuncotationFactory.java:474)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationsByAllTranscripts(GencodeFuncotationFactory.java:475)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:530)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:233)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:201)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:172)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:147)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:157)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:903)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:857)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3500m -jar /root/gatk.jar Funcotator --data-sources-path /cromwell_root/datasources_dir --ref-version hg38 --output-file-format VCF -R gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -V gs://fc-96b07fd2-b95b-4512-8cc3-d1b1271cfdf4/8d01203d-dc60-44e1-bb12-3c69d5cba8a8/Mutect2/a7e81c79-c696-4a6c-8dbf-c209f6b1b2c4/call-Filter/D_3969180_200714149.chr-filtered.vcf -O D_3969180_200714149.chr-filtered.annotated.vcf --annotation-default normal_barcode: --annotation-default tumor_barcode:D_3969180_200714149 --annotation-default Center:Unknown --annotation-default source:Unknown --transcript-selection-mode ALL

The offending variant from the input vcf file is:

chr13 113640223 . GACGAGGAGGACGATGACT G . clustered_events;haplotype;panel_of_normals CONTQ=93;DP=69;ECNT=3;GERMQ=78;MBQ=37,37;MFRL=170,98;MMQ=60,60;MPOS=8;PON;POPAF=7.30;ROQ=93;SEQQ=87;STRANDQ=93;TLOD=15.62 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:60,9:0.083:69:23,5:24,3:0|1:113640223_GACGAGGAGGACGATGACT_G:113640223:40,20,5,4

Thanks for any help!