Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Reading a vcf - genotypes

    Hi, I am trying to understand the genotype calls in my vcf, a trio.
    Looking at one variant of interest, the calls are:
    Dad Mum Kid
    0/2 2/1 1/1

    How can the kid be 1/1?
    The full information is:

    FORMAT
    GT:ADP:GQ:PL

    Dad
    0/2:9,3,0:16:19.63:134,0,98,27,20,47

    Mum
    145 2/1:8,4,0:20:15.38:197,15,52,44,0,41

    Child
    1/1:7,2,0:11:1.37:113,31,61,9,1,0


    Thanks for any help.

  • #2
    Note the GQ value, which is quite low for the child. You might consider filtering by quality.

    You will run into this sort of thing on occasion. The general causes are (1) sequencing error (2) genotype call error (3) sample swap (this should be pretty obvious though) (4) non-paternity. The last one is more common than you would think (1-3% of cases where there's otherwise no dispute of paternity), though you'll again end up with a lot of sites like this.

    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