Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • heterozygosity and allele balance in NGS doubt

    Hi,

    I have data from a target enrichment on a few human genes, of course sequenced through NGS. Enrichment, sequencing and data analysis were performed by a private genomic service.

    In the VCF file some variants show an allele frequency around 1-2%, but their locus is called as heterozygous. Isn't the variant presence too low to call it as heterozygous?

    I am not too acquainted with these kind of analysis, so I am a little confused by this. Could someone please help me out?

    Thanks a lot in advance.

    Marco

  • #2
    Why not do some filtering on the data ? Think vcfutils will do this for you.

    Generally people might take variants with an allele frequency cutoff of around 22% to be genuine heterozygotes. Sometimes you get a nice 50/50 ratio, but you miss out on a lot of data if you stick to very strict thresholds.

    Certainly reporting 1-2% AF as heterozygotes is not great analysis.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM
    • seqadmin
      Multiomics Techniques Advancing Disease Research
      by seqadmin


      New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

      A major leap in the field has
      ...
      02-08-2024, 06:33 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:12 AM
    0 responses
    19 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-23-2024, 04:11 PM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2024, 08:52 AM
    0 responses
    73 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-20-2024, 08:57 AM
    0 responses
    65 views
    0 likes
    Last Post seqadmin  
    Working...
    X