Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • convert vcf to hapmap

    I was trying to use SNPhylo software.
    I needed to combine multiple SNP vcf files together or use combined hapmap file.
    Is there any way to get single vcf or hapmap file with multiple samples together?

  • #2
    bcftools-merge? http://vcftools.sourceforge.net/htslib.html#merge

    Comment


    • #3
      Originally posted by GenoMax View Post


      Thanks I tried vcf-merge

      Comment


      • #4
        @sandesh
        i am trying to run SNPhylo.do i need all the VCF, Simple SNP file and hapmap file ??or i need just one of these files.pls help

        Comment


        • #5
          I fed SNPhylo only a VCF file and it ran smoothly. If you use SNPhylo, please check the sam headers, it seems SNPhylo only accept number as chromosome header (e.g. >1 but not >chr1) at least for old SNPhylo version (2014.....). Hope it helps.

          Comment


          • #6
            SNPhylo

            hi yzzhang, i appreciate your help. I have this project to find SNPs across 5 different population and build a phylogenetic tree. so, for my VCF file should i combine all the SNPs from all population into one VCf file and then run SNPhylo??

            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
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            9 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            51 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