Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • New to SNP analysis

    Hi,

    I'm quite new to SNP analysis and I there's something I think should be simple to do but I cannot find any existing programs to help me. I want to find all the SNPs that are candidates for differences between two bacterial strains. I've tried programs like Harvest Suite, which is nice for viewing the SNPs but it can't output what I need: i.e. a list of SNPs that are fixed and different between the groups (akin to private alleles in a classical mapping). I could view them all manually, but that seems silly when it should be a simple thing to automatically output.

    I'm hoping I don't have to write a script to parse the VCF files.. I hate those files..

    Thanks for any help,

    Susan

  • #2
    GATK (Select Variants) or BedTools (subtract) can be used to filter multiple VCF files for common or unique SNPs.

    Comment


    • #3
      vcftools/bcftools are additional options to manipulate VCF files.

      Comment


      • #4
        SNP interactions

        Hi,

        ok, thanks yes I saw those but they didn't quite do what I wanted, So I wrote my own python script, but then I was told from the person who gave me the that they have continuous variable data for samples, not categories as I thought, hence I now need to actually correlate presence / absence of SNPs against multiple phenotype measurements.

        But again, I have come up blank on existing programs.. is there anything that can do this? I guess that when a SNP has multiple states then a correlation has to be done for each separately so its not just as simple as one correlation per line of the .vcf.

        Also what about interactions between snps? I have 127,000 in my dataset.. that's a lot of interactions to test!

        Thanks for any advice,

        S.

        Comment


        • #5
          I have just found something called GCTA that I think will do what I need.

          Comment


          • #6
            When you generate the mpileup file, try use varscan2, it is very handy.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Current Approaches to Protein Sequencing
              by seqadmin


              Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
              04-04-2024, 04:25 PM
            • 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

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            25 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            27 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            24 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            52 views
            0 likes
            Last Post seqadmin  
            Working...
            X