Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Filter VCF file to have just one variant per contig

    Hello, I have a multi-sample VCF file, with about 4000 contigs/loci represented. Many of these contigs contain multiple SNPs, meaning the SNPs are linked to one another in this case. However, some of my downstream analyses do not handle linked markers well, so I would like to be able to filter my VCF file so that I am left with a single SNP per contig. If there were a way to randomly select one SNP per contig, that would be great. Any ideas about how to achieve this? As far as I can tell, VCFtools does not allow this.

  • #2
    vcftools does have a --thin option, and if you set it to the maximum contig size then there will be only 1 SNP per contig (--thin 100000, for example).

    It may select the first SNP in the contig, though.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment


    • #3
      Great, thanks SNPsaurus, this is working nicely. I would still like to do a 'random SNP per locus' option, and compare results to what I'm getting with this 'first SNP per locus' method, but this might require some more advanced programming skills.

      Comment

      Latest Articles

      Collapse

      • 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
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-14-2024, 06:13 AM
      0 responses
      33 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-08-2024, 08:03 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-07-2024, 08:13 AM
      0 responses
      80 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-06-2024, 09:51 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X