Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • VarScan: somatic mutations in heterozygous sites?

    Does VarScan2 find somatic mutations that arose in loci where norm was heterozygous? As far as I can tell, it classifies somatic changes as "Somatic" (but that seems to only include homozygous normal) and "loss of heterozygosity", where normal was hetereozygous, and tumor is homozygous". What happens if normal was heterozygous, and tumor has 3 alleles (one novel)? I don't seem to be able to find such sites in VarScan output.
    Thank you,
    Elena

  • #2
    Are there situations where true, validated somatic mutations arise at the position of heterozygous SNPs? My expectation is that most such situations would represent artifactual calls, not real events.

    In your example, the normal would be called heterozygous, and the tumor would be called heterozygous (if a variant allele met calling criteria). The most-supported variant allele in tumor would be taken as the consensus. If it's the same as the normal variant allele, the call will be Germline. If it's a third allele, VarScan will call it "Unknown" because this is an unexpected situation. Running VarScan somatic with the --validation 1 parameter will tell you.

    You could also investigate by running VarScan mpileup2cns instead. Feel free to e-mail me the pileup outputs if you'd like to discuss further.

    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
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X