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.


I have been trying to get my hands on help docs or command line examples for the indelocator ...
It does not seem to have any support yet still part of the tool for cancer sample analysis.
Do you have any recommendations? If it is not recommended then why make it public?

Many of us would like to understand how to run it, we can probably do our own filtering on verbose output.



Best Answer


  • barakbarak Member

    OK. thanks a lot.
    Looking fw for a new indel caller :)

  • VewehrVewehr Czech RepublicMember

    So what is the best tool for somatic indel detecting available now? I am a newbie in this area of expertise and I am searching for some tool to call somatic indels in our set of data. Thank you.

  • dklevebringdklevebring Member

    My two cents: I use IndelLocator (the one which is available) and pindel and filter results using Fisher's exact test, with a hard cutoff of the normal allele fraction.

    @kcibul Any timeline for when the successor might become available? Are we talking month(s) or year(s)? A very very rough estimate would be great. Even a beta version I think would benefit many in the community. Thanks.

  • barakbarak Member

    I use a Shimmer at the moment. Roughly the same approach using samtools.

Sign In or Register to comment.