Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Select a single snp in a contig

    Hi everybody,

    I have multiple SNPs per contig in a fasta file. I would like to get just one SNP per contig to reduce the effects of linkage.

    How can I do this?


    Already, thank you.

  • #2
    Hi Rhewter.. I hope you are well...
    The main question before try to help you is understand what SNP do you want to keep. Probably you need to choice some SNP trait like depth or allele frequence and based on some SNP trait decide for one. Do you have potitions for each of them?

    Comment


    • #3
      Originally posted by arthurmelo View Post
      Hi Rhewter.. I hope you are well...
      The main question before try to help you is understand what SNP do you want to keep. Probably you need to choice some SNP trait like depth or allele frequence and based on some SNP trait decide for one. Do you have potitions for each of them?
      Hello Arthur,

      I am fine and hope you are too.
      I just got using R scripts + vcftools. The selection of a single SNP by contig was made using the highest quality grade for the site. I had already filtered through depth and I think for allele frequency is not a good idea because I have only five individuals. But thanks anyway.

      One more question ... You've used the snpEff? It has added a new reference to the configuration file?

      Hugs from Brazil.

      Comment


      • #4
        If you still have the vcf then vcftools allows you to "thin" the SNPs by removing some.

        --thin <integer>

        Thin sites so that no two sites are within the specified distance from one another.
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

        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, 02-28-2024, 06:12 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-23-2024, 04:11 PM
        0 responses
        70 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2024, 08:52 AM
        0 responses
        77 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-20-2024, 08:57 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X