Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Latest GATK and DINDEL

    The latest version of GATK does not appear to have a DINDEL option for the indel caller. Is DINDEL the default method for indel calling with the GATK Unified Genotyper?

    Has anyone compared the two tools to confirm this?

  • #2
    Originally posted by genericforms View Post
    The latest version of GATK does not appear to have a DINDEL option for the indel caller. Is DINDEL the default method for indel calling with the GATK Unified Genotyper?

    Has anyone compared the two tools to confirm this?
    The current method is called INDEL rather than DINDEL, and it's not the same. See this reply to a similar query from Eric Banks at GSA:



    "In our own tests the newest model performs best, which is why we transitioned over to it. To be honest, though, the genotype likelihoods model for indels is still in constant flux and we are continuously improving it...The reason why we renamed it, by the way, is that this newer model is not really related to the actual "Dindel" software while the previous one was very much inspired by it. We felt that it wasn't fair to the authors of Dindel to continue naming it after their tool."

    Comment


    • #3
      Originally posted by RDW View Post
      The current method is called INDEL rather than DINDEL, and it's not the same. See this reply to a similar query from Eric Banks at GSA:



      "In our own tests the newest model performs best, which is why we transitioned over to it. To be honest, though, the genotype likelihoods model for indels is still in constant flux and we are continuously improving it...The reason why we renamed it, by the way, is that this newer model is not really related to the actual "Dindel" software while the previous one was very much inspired by it. We felt that it wasn't fair to the authors of Dindel to continue naming it after their tool."
      I appreciate this. So it seems the method is similar or the same, but Eric and his group are continuously updating the error model? So I think I will have to compare both to see how they perform on my data.

      Thanks again for the post.
      Last edited by adaptivegenome; 11-24-2011, 01:06 PM. Reason: typo

      Comment


      • #4
        Originally posted by genericforms View Post
        So it seems the method is similar or the same, but Eric and his group are continuously updating the error model?
        Just to clarify, my understanding is that the DINDEL option they were using for the Unified Genotyper a few months ago was indeed similar to the freestanding Dindel program from Sanger, but the INDEL option they're now using is based on a different model (which continues to evolve). So all the more reason to do the comparison you suggest (and post the results!).

        Comment


        • #5
          Originally posted by RDW View Post
          Just to clarify, my understanding is that the DINDEL option they were using for the Unified Genotyper a few months ago was indeed similar to the freestanding Dindel program from Sanger, but the INDEL option they're now using is based on a different model (which continues to evolve). So all the more reason to do the comparison you suggest (and post the results!).
          Yes, I will post what I find...

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM
          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 06:37 PM
          0 responses
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          51 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X