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
        Best Practices for Single-Cell Sequencing Analysis
        by seqadmin



        While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
        06-06-2024, 07:15 AM
      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        05-24-2024, 01:16 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 06-07-2024, 06:58 AM
      0 responses
      179 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-06-2024, 08:18 AM
      0 responses
      227 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-06-2024, 08:04 AM
      0 responses
      184 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-03-2024, 06:55 AM
      0 responses
      18 views
      0 likes
      Last Post seqadmin  
      Working...
      X