Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • heterozygous structural variants

    Is there any one knows that it is possible to get heterzygous SVs from the output of breakdancer, pindel etc? Or are the output from the 2 softwares all homozyous?

  • #2
    Moved to a more appropriate forum.

    Comment


    • #3
      Breakdancer reports all variants for which it has enough support, in terms of then number of discordant read pairs, and does not call the genotype. Therefore, I think the output probably consists of both homo- and hetero-zygous variants.

      You might want to look into the new GASVPro, which tries to call the genotype of variants based on depth of coverage around the breakpoints:

      Sindi, S. S., Onal, S., Peng, L., Wu, H.-T., & Raphael, B. J. (2012). An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biology, 13(3), R22. doi:10.1186/gb-2012-13-3-r22

      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
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 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
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X