Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • graubner277
    Junior Member
    • Oct 2015
    • 2

    Strange VAF distribution across SNP positions in WGS sample

    Hi everyone,

    I have a germline sample that underwent whole genome sequencing at 30x on Illumina Hiseq. After extracting the VAFs at all 1000 Genomes SNP positions, it seems that the data is strangely noisy.

    - If you plot a histogram of VAFs from normal samples, you would expect a peak at 0.5 for heterozygous variants and 1.0 for homozygous variants, with some sort of distribution in between for sequencing noise. However, in this sample there is almost a uniform distribution from 0 to 0.8 and a peak at 1.0 (see attached figure).

    - This is also reflected when I plot the VAFs at these SNPs from the germline sample (in blue) and a matched tumor sample (in red). In a normal-looking sample, the blue dots should cluster around 0.5 on the y-axis, and the red dots separate where there is a CNV. In this weird sample, you can see that the blue dots basically do not cluster around any VAF, whereas the matched tumor sample looks fine.

    I've compared this sample with other samples, and there is no significant difference in coverage, insert size, GC content, ACGT content, indels, base quality or mismatch distributions. Anyone have any idea what might give rise to such noisy data or anyone seen a similar case before? Thanks!
    Attached Files
  • Bukowski
    Senior Member
    • Jan 2010
    • 388

    #2
    Do you have more SNP calls in your 'weird' sample?

    Contamination perhaps?

    Comment

    • graubner277
      Junior Member
      • Oct 2015
      • 2

      #3
      The number of SNP calls was similar to others as well, so was the Ti/TV, Het/Hom ratio, % in dbSNP, % in Genes etc. I did not notice the noise from any of the sequencing QC statistics or SNP calls until I did a plot of the VAFs.

      I was wondering if it was perhaps contaminated with another sample, but I felt that there would be bands or multiple VAF peaks if there was say 1 other sample. It would have to be many samples together to get such a VAF distribution I think? And this is the only sample I have out of 30 that looks like that.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Pathogen Surveillance with Advanced Genomic Tools
        by seqadmin




        The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
        03-24-2025, 11:48 AM
      • seqadmin
        New Genomics Tools and Methods Shared at AGBT 2025
        by seqadmin


        This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

        The Headliner
        The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
        03-03-2025, 01:39 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-20-2025, 05:03 AM
      0 responses
      49 views
      0 reactions
      Last Post seqadmin  
      Started by seqadmin, 03-19-2025, 07:27 AM
      0 responses
      57 views
      0 reactions
      Last Post seqadmin  
      Started by seqadmin, 03-18-2025, 12:50 PM
      0 responses
      50 views
      0 reactions
      Last Post seqadmin  
      Started by seqadmin, 03-03-2025, 01:15 PM
      0 responses
      201 views
      0 reactions
      Last Post seqadmin  
      Working...