Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cnv annotation

    Hi,
    I used ExomeCNV and FREEC on my tumor-normal matched exome sequencing samples to discover copy number variations. Now I need to combine and annotate the results.

    What kind of tools would you suggest for the task ?

    Can Annovar be used for annotation purpose of CNV files?

    Thanks


    Suleyman

  • #2
    • CNV/SV merging:
      To merge/combine the common CNV detected by your different callers, I would consider CNV that share a 70% reciprocal overlap measured by length and position (> 70% shared length) (as done in DGV).

    • CNV/SV annotation:
      I suggest using AnnotSV for SV/CNV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information).
      You can look at the following post describing the annotSV tool:
      http://seqanswers.com/forums/showpos...87&postcount=4

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    22 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    46 views
    0 likes
    Last Post seqadmin  
    Working...
    X