Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Geneious SNP detection parameter setting

    Is there anyone here using Geneious. Not quite sure about the parameters setting on "Find Variations/SNPs." Here is what I did in my project.

    Any suggestion is welcome. thx



    Last edited by arkilis; 10-03-2013, 05:09 PM.

  • #2
    I'm quite in it those days, but I'm not using Geneious. However, this is what I can see from the printscreen above:

    1. Minimum coverage: I would set it higher, perhaps around 10. That's the number of times your SNPs will be covered. Logically, if you have only two reads covering the SNPs, that chance that both reads are errors is quite bigger than if you had 20 reads covering the same base.

    2. Minimum Variant Frequency: for every SNPs that your program will find, you will have a certain number of reads that match the reference sequence, and a certain number of reads that match the alternative (SNP) call. Minimum Variant Frequency of 0.25 means that you have 1 alternative call and 3 reference calls (1/4=0.25). You can set it low in the beginning, but keep in mind that higher values are "better" for accurate calls.

    3. Maximum Variavnt p-value: you control the risk of the call being made purely by chance. Go logically and set it according to the risk you want to take.

    I think the rest of the options speak for itself.

    Comment


    • #3
      Originally posted by ThePresident View Post
      I'm quite in it those days, but I'm not using Geneious. However, this is what I can see from the printscreen above:

      1. Minimum coverage: I would set it higher, perhaps around 10. That's the number of times your SNPs will be covered. Logically, if you have only two reads covering the SNPs, that chance that both reads are errors is quite bigger than if you had 20 reads covering the same base.

      2. Minimum Variant Frequency: for every SNPs that your program will find, you will have a certain number of reads that match the reference sequence, and a certain number of reads that match the alternative (SNP) call. Minimum Variant Frequency of 0.25 means that you have 1 alternative call and 3 reference calls (1/4=0.25). You can set it low in the beginning, but keep in mind that higher values are "better" for accurate calls.

      3. Maximum Variavnt p-value: you control the risk of the call being made purely by chance. Go logically and set it according to the risk you want to take.

      I think the rest of the options speak for itself.
      Thanks for your reply.

      1. minimum coverage. I think it is more depended on platform. For NGS data, you are right. 10 reads at least is more secured. For Sanger, I think two might be enough. Since Sanger data always has a good quality.

      2. What you saying makes much sense.

      3. HARD PART! since I don't know a proper value here. If I decrease the value, less 'SNPs' will come out. Hope those who play Geneious can see this post and provide with a moderate value..

      Thanks!
      Last edited by arkilis; 10-03-2013, 08:05 PM.

      Comment


      • #4
        Hey Arkilis,

        Geneious is a commercial tool. So, i dont think much people use it.

        But, the option parameters are more or less same in all available variant calling tools.

        Say, for example VarScan. just have a look into it.

        Comment


        • #5
          Originally posted by vishnuamaram View Post
          Hey Arkilis,

          Geneious is a commercial tool. So, i dont think much people use it.

          But, the option parameters are more or less same in all available variant calling tools.

          Say, for example VarScan. just have a look into it.
          That is a good idea.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Genetic Variation in Immunogenetics and Antibody Diversity
            by seqadmin



            The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
            11-06-2024, 07:24 PM
          • seqadmin
            Choosing Between NGS and qPCR
            by seqadmin



            Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
            10-18-2024, 07:11 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 11-08-2024, 11:09 AM
          0 responses
          57 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 11-08-2024, 06:13 AM
          0 responses
          38 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 11-01-2024, 06:09 AM
          0 responses
          35 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-30-2024, 05:31 AM
          0 responses
          23 views
          0 likes
          Last Post seqadmin  
          Working...
          X