Mutect2 Funcotator interval error

Answered

Follow

Elise Valkanas (she/her)

• November 09, 2021 15:39
• Edited

I am running Mutect2 (us.gcr.io/broad-gatk/gatk:4.1.7.0) on Terra using in PON mode for a single hg38 WGS CRAM. I have cloned the example Terra workspace and updated the reference info and all somatic workspace files to hg38, but am having a problem with Funcotator.  It looks like Funcotate isn't properly handling the case where the variant is close to the start of the contig and is making the start of the reference window negative rather than the start position of the contig. The log file is too large to post in its entirety, but here is part of the error with Funcotate:

java.lang.IllegalArgumentException: Invalid interval. Contig:chrUn_KI270468v1 start:-1 end:18 
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:733) 
at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:59) 
at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:35) 
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.createReferenceSnippet(FuncotatorUtils.java:1439) 
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createIgrFuncotation(GencodeFuncotationFactory.java:2437) 
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createIgrFuncotations(GencodeFuncotationFactory.java:2363)

I have tried increasing memory with no change to the tool behavior. I would like to get to the bottom of this issue. I have asked a similar question on the Terra forum and was referred here as it seems to be an issue with the functionality of the Funcotator tool. 

Would appreciate any help getting to the bottom of this. 

Thanks!
Elise

0

• 

  Genevieve Brandt (she/her)

  • November 09, 2021 17:13

  Hi Elise Valkanas (she/her),

  Thanks for writing into the forum with this issue, I can help you out to figure out what is going on here.

  I found a previous forum post where a user was having the same issue. It looks like the problem was determined to be a bug in 4.1.7.0, however, the github ticket has not been solved yet: https://github.com/broadinstitute/gatk/issues/6598.

  I can look into the problem further to try to determine a workaround. Could you verify that this issue persists in the latest version of GATK (4.2.3.0) with the new data sources? Please also provide your Funcotator command line and complete Funcotator program log.

  Best,

  Genevieve

  0

  Comment actions Permalink
• 

  Elise Valkanas (she/her)

  • November 11, 2021 18:10

  Hi Genevieve, 

  Thanks! Since this is a featured workspace I didn't think that the version of GATK would need to be updated, but looks like doing that and changing the Funcotator files did the trick. Thanks for the help!

  Elise

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • November 12, 2021 17:01

  Thanks for the update Elise and glad your problem is resolved!

  GATK 4.1.7.0 is a stable release so we still are using it for featured workspaces. I'll forward this information to my colleagues who work on those featured workspaces so that they can prioritize getting a new version of GATK tested.

  0

  Comment actions Permalink
• 

  Elise Valkanas (she/her)

  • January 19, 2022 17:00

  Hi Genevieve, 
  
  I just wanted to follow up and say I am re-running this workflow and running into the same interval failures for Funcotate regardless of the gatk version. They seem to all fail on alt contigs so supplying an interval file with only primary contigs solved the error I was having. 

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • January 19, 2022 19:23

  Thank you for the update Elise Valkanas (she/her)!

  0

  Comment actions Permalink

Please sign in to leave a comment.