Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Variants inside and outside of target region - what's the difference?

    Hello:

    I am trying to understand whether there is some drastic difference between on-target and off-target reads. I assume that even if there is a true variant outside of target region, it is not of interest anyway. Apart from that, is there any difference between the two sets of reads and the variants detected by such reads?

    In terms of (quantitative) metrics that can be computed for VCF files, is there any difference between the variants inside and outside of target region? For instance, if I were to compute an average depth across variants inside the target region, will it be higher than the depth outside the target region?

    Thanks in advance,
    Nik

  • #2
    I assume you are talking about exome-capture?

    There is no important difference between on- and off-target reads. Variants outside target regions may be of interest, though it's less likely; and of course 99.99% of variants inside the target are of no interest, but presumably they will tend to be more interesting than the ones outside the targets. Note that the gene annotations are continuously evolving as new genes and isoforms are discovered, while baits for capture kits may be based on annotation from many years earlier.

    If the capture was successful, then yes, the coverage will be much higher within the targets than outside.

    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