Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GATK- haplotypecaller or unifiedgenotyper?

    Hi all,
    I have been looking at the GATK documentation at in the best practices it says:

    HTML Code:
    We believe the best possible caller in the GATK is the HaplotypeCaller
    I don't really understand why the haplotype caller is better than the unifiedgenotyper. If I am going to be doing 2 whole genomes (~40X each) on a paired tumor/normal, is the haplotypecaller the best option? I had used the unifiedgenotyper in the past.

    Thanks

  • #2
    To answer the question you are really asking and not the question in the title, if you are looking for somatic mutations, then neither is likely to be the best tool. You might consider looking at somatic variant callers such as muTect, strelka, somaticsniper, or VarScan2.

    Comment


    • #3
      The Tumor is not going to be diploid. This will be incompatible with HaplotypeCaller and high ploidy slows UnifiedGenotyper way way down. Just make sure your caller is meant for pooled or high pliody samples. As for the above suggestions, i haven't used them. I use SNVer right now for viral population projects, it seems to go the trick and is painless to get up and running.
      --Please take everything thing I say with a grain of salt, because, if grad school has taught me anything, it's that I'm an idiot--

      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
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      66 views
      0 likes
      Last Post seqadmin  
      Working...
      X