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.

Writing a custom org.broadinstitute.gatk.tools.walkers.annotator.InfoFieldAnnotation

lindenblindenb FranceMember ✭✭

I'm playing with the package org.broadinstitute.gatk.tools.walkers.annotator and I wonder if I can write the following custom variant annotator:

I've got a set of tabix-ed files in a directory (one txt.bgz per chromosome) and I want to peek the information from those files.

  • Can I specify an external resource like a directory for -T VariantAnnotator ? If no, can I add something like a java annotation to specify a new cmd-line argument in my CustomAnnotation.java ? (I don't want to modify VariantAnnotator.java )
class CustomAnnotation  extends InfoFieldAnnotation  {
@Argument(fullName = "mydir", shortName = "mydir", doc="My directory of tabix files", required=true)
File dir;

}

  • Parallelism : if my CustomAnnotation open some tabix files, should I care about parallelism ? (e.g: open the tabix file for each thread )

  • there is a initialize method in VariantAnnotatorAnnotation but no dispose ?

Thanks !

Pierre

Issue · Github
by Sheila

Issue Number
1538
State
open
Last Updated

Best Answer

Answers

  • lindenblindenb FranceMember ✭✭

    Ok thank you Geraldine. I was just curious if I could implement a custom annotator using the gatk. I'll stick to htsjdk-only :-)

Sign In or Register to comment.