Hi, FireCloud team
I ran into a problem recently coming from Funcotator. I initially run Mutect2 coupled with Funcotator on FireCloud, GATK 4.0.4.0 version (my data is aligned with hg38), but it throw out some error. And I also tried Funcotator locally and it produces the almost identical error, see below. The only difference is the number after String index out of range.
org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 27.56 minutes. Runtime.totalMemory()=12031361024 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) .....
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.
Thanks,
Zhouwei