Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Annotating indels

    Hello,

    I apologize for asking what may be a really silly basic question.

    I identified cancer specific SNPs with GATK's Somatic Indel Detector, and then used the verbose output file to retrieve SNPs in coding regions with no or low counts in normal. These I then visually validated in IGV. However, my data is in a text file (well, excel file).

    The indel calling part looks like:
    Chrom Last Ref base Last event base Event
    1 120612002 120612004 -GG
    7 151927358 151927358 +A
    X 66766356 66766377 -GGCGGCGGCGGCGGCGGCGGC
    This is directly from the verbose output (sans header line as explanation). -GG means a deletion of GG. +A means an insertion of A at that location.

    I've tried taking this into Oncotator, but that requires me to change the base pair numbers and how the event is labelled. Worse, all it does is say "p.P6fs" and "Frame Shift Del." I'm glad to know the amino acid, but I need to know if it creates a stop codon or what the base is changed to, etc.

    I've seen people suggest SnpEff, and GATK recommends that too. However, SnpEff has deprecated their txt input. Plus, I have no idea how to get what I listed above into their recommended input format without what seems like a lot of manual work and possibly taking it into Oncotator first to get the strand.

    Does anyone have any suggestions?

    Thank you,
    Rose

  • #2
    You could try Annovar but you will have to change the input a little bit.
    Jane

    Comment


    • #3
      It looks like Annovar also just labels things like p.G12fs.

      Is what I'm thinking of just not done?

      Comment


      • #4
        What exactly do you mean by what a base is changed to when talking about indels?

        Comment


        • #5
          Say the original sequence at a point is TGT (Cys). An insertion occurs such that it's now TG[T]T. That would still be a Cysteine at that location, though it will likely mess up everything downstream. However, that might depend on what's downstream.
          If the insertion instead is TG[A]T, that's an immediate stop codon.

          So I would like an annotation program that tells me if the current codon is changed, if a stop codon is created downstream, and optimally whether the indel is deleterious overall (for example, from protein folding) if something like PPH2 or Mutation Assessor is incorporated.

          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, 03-27-2024, 06:37 PM
          0 responses
          15 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-27-2024, 06:07 PM
          0 responses
          13 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          55 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          70 views
          0 likes
          Last Post seqadmin  
          Working...
          X