Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Pindel and GATK AD Concordance

    I was hoping to get some advice on working with the AD field for variants in VCFs produced by Pindel and Pindel2VCF.

    My lab has a variant calling pipeline that uses GATK's UnifiedGenotyper for calling SNVs and small Indels, as well as using Pindel to call deletions and short insertions. As part of our VCF filtering, we remove variants with an Variant Allele Fraction below a certain threshold. However, it has been brought to my attention by other members of the lab that when Pindel and UnifiedGenotyper call the same variant, they have different AD values and so different VAF values (I'm not sure if it's relevant, but the AD for UnifiedGenotyper is the same as found in IGV).

    Normally the difference is small enough that it doesn't affect our filtering, but there have been some cases where a variant called by both branches of the pipeline has an VAF greater than our cutoff threshold in one VCF, but has an VAF lower than threshold in the other VCF. To avoid this issue, which value for AD should I be using for calculating VAF? The AD from UnifiedGenotyper, or the AD from Pindel?

    Thanks in advance for any suggestions.

  • #2
    I've also posted this thread on BioStars (https://www.biostars.org/p/256882/)

    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