Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • discrepancies in allele frequencies between 1000 genomes and 5400 exomes

    Using ANNOVAR summary routine I have got a exome_summary.csv file that contains different columns with 1000 genomes and 5400 exomes frequencies with some empty cells. I asume that empty cells correspond to SNPs that were not found in any of these databases. However there are cases where you get frequencies either in 1000 genomes or 5400 exomes but not in the other database. I would understand it if the alllele frequency in the alternate database would be very low, but there are cases where this frequency can be up to 80%. Does anyone know what is the reason for these big discrepancies between these databases?

  • #2
    The 1000G and 5400ESP projects used different pipelines for sequencing, read mapping and and variant calling, so at least some of the major discrepancies between the listed allele frequencies are due to different quirks in their respective pipelines. For example, each pipeline might consistently map ambiguous reads to a different site in a repetitive or low-complexity region, giving the variant calls in that region a high frequency in one database but not the other.

    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, 03-27-2024, 06:37 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X