Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

How can I use CombineVariants with Queue

Hi,

Queue is unable to build a proper job graph if I do something like this:

combineVariants.variant +:= gtHaplotypeCaller.out + ":HC"
combineVariants.variant +:= gtUnifiedGenotyperSNP.out + ":UGSNP"
combineVariants.variant +:= gtUnifiedGenotyperINDEL.out + ":UGINDEL"
combineVariants.genotypeMergeOptions = GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE
combineVariants.priority = "HC,UGSNP.UGINDEL"

The problem seems to be by not using exactly the output values from the other jobs, Queue is unable to properly link output from required jobs before CombineVariants.

I also tried:

combineVariants.variant +:= gtHaplotypeCaller.out
combineVariants.variant +:= gtUnifiedGenotyperSNP.out
combineVariants.variant +:= gtUnifiedGenotyperINDEL.out
combineVariants.genotypeMergeOptions = GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE
combineVariants.priority = "variants,variants2,variants3"

In this case I get:

##### ERROR MESSAGE: Invalid command line: Argument rod_priority_list has a bad value: Not all priority elements provided as input RODs: variants,variants2,variants3

Any recommendation on how to run CombineVariants using Queue and merge type PRIORITIZE.

Thanks,
Carlos

Best Answer

Answers

  • CarlosBorrotoCarlosBorroto Member ✭✭

    That did it. Thanks!.

    Note: There is a small typo. Should be "HC,UGSNP,UGINDEL" instead of "HC,UGSNP.UGINDEL".

Sign In or Register to comment.