Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Funcotator error

zwzhangzwzhang Member, Broadie
edited June 2018 in Ask the GATK team

Hi, GATK 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, 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.

Thanks,
Zhouwe

Answers

Sign In or Register to comment.