Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SNP and indel calling methods

    Dear all,

    I'm wondering how to do a good SNP and indel calling. There are a lot of aligners each contains different parameters and gives different results.
    There is always the dilemma between results that is significant but partial and results that are wide but contain false-positives.

    In 1000-genome project site they say about SNP calling methods:
    "We found empirically that, given the state of current methods, the consensus of multiple primary call sets from different methods proved of higher quality than any of the primary call sets themselves. ... Overall, genotypes obtained through a consensus procedure are estimated to have 30% fewer errors than those generated by any single caller."

    - I wonder if there's a tool that does alignments with different parameters/ tools and then merges the results using statistical methods?

    - What would you say are the best SNP calling tools? (bowtie? GATK? samtools? others?...)

    Thanks,
    Rachelly.

  • #2
    I haven't heard of a consensus SNP aligner which parses the output from multiple SNP callers, you'll probably not find this too tricky to do yourself.

    We have had good results with the VarScan program, but have yet to really test the predictions in the wetlab. Previous results from the ELAND aligner and custom perl scripts using quality sums weren't too great to validate, that is, there were a lot of surprising false positives despite high-ish coverage (10+).

    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
    11 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