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Hi, FireCloud team
Sorry for the duplicated question. I just want to update the format.
I ran into a problem recently coming from Funcotator. I initially run Mutect2 coupled with Funcotator on FireCloud, GATK 184.108.40.206 version, but it throw out some error. And I also tried run Funcotator locally and it produces the almost identical error, see below
[June 6, 2018 1:47:32 PM EDT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 12.63 minutes. Runtime.totalMemory()=12082741248 java.lang.StringIndexOutOfBoundsException: String index out of range: -61 at java.lang.String.substring(String.java:1967) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createUtrFuncotation(GencodeFuncotationFactory.java:1088) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnTranscript(GencodeFuncotationFactory.java:601) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:529) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:276
I know Funcotator is still in beta version, but want to ask you help me debug this problem and I am also wondering is there any more stable Funcotator.