Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • adaptivegenome
    Super Moderator
    • Nov 2009
    • 436

    #1

    Describing tandem repeats using VCF 4.1

    I am writing out tandem repeat variation to VCF format and I would like to use the best possible identifier.

    From VCF 4.1, docs state:

    "The ID field indicates the type of structural variant, and can be a colon-separated list of types and subtypes. ID values are case sensitive strings and may not contain whitespace or angle brackets. The first level type must be one of the following:

    DEL Deletion relative to the reference
    INS Insertion of novel sequence relative to the reference
    DUP Region of elevated copy number relative to the reference
    INV Inversion of reference sequence
    CNV Copy number variable region (may be both deletion and duplication)
    The CNV category should not be used when a more specific category can be applied. Reserved subtypes include:

    DUP:TANDEM Tandem duplication
    DEL:ME Deletion of mobile element relative to the reference
    INS:ME Insertion of a mobile element relative to the reference"

    Certainly if we have a repeat like TATATA, mutations could be described as INS or DEL but I think there should be separate identifier for tandem repeats.

    Thoughts?

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-22-2026, 11:13 AM
0 responses
42 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 10:48 AM
0 responses
33 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
44 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
45 views
0 reactions
Last Post SEQadmin2  
Working...