Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Look for somatic mutation from Ion Proton Exome Sequencing

    I've used Strelka and MuTect to find somatic mutations in SOLiD and Illumina data. They worked pretty well, but not so well for Ion Proton Exome (yes, a ton of homopolymer deletions and even more senseless insertions).

    Does anyone have experience with somatic variant calling from Ion Proton or Ion Torrent?

    Thanks in advance!

  • #2
    I am currently in the process of validating a bunch of somatic mutations I detected in some exomes using MuTect and some other algorithms. I've been doing extensive research into the tools available for several months - some programs will under call (I've found that mutect severely under calls) and some will over call..

    You'll find more problems with the indels rather than the SNVs.. The good news is that indel calling with a program like VarScan2 is not missing the true positives, you just get a ton of false positives and it's hard to differentiate between them.

    (Sorry - only just saw this post)

    Comment


    • #3
      @sophiespo
      Any results from that exercise? What worked best for you in the end? Would be interested to hear.

      BR
      daniel

      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
      7 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      7 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