Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • need help with converting VCF to GTF/GFF format

    Hi,
    I need to convert my vcf (from ftp://ftp.ncbi.nih.gov/snp/organisms...9606/VCF/v4.0/) file to gff/gtf format to be able to use it for annotating my refseq with SNPs.
    Is there any tool I could use for converting that file?
    Thanks

  • #2
    These sorts of conversions are rather tricky because it is difficult to construct a set of standard conversion decisions that will please everyone's specific demands. VCF to BED/GFF is doable with an awk script. BED and GFF are essentially interchangeable with awk as well. GFF/BED to VCF is not really doable unless the necessary VCF info is already tracked in the BED or GFF.

    This is what I found on another forum. I do not think there is a tool that does this for you. I have searched for scripts, but I did not come across any. As it was written is that post, the best way would be to build your own script.

    Andrei

    Comment


    • #3
      I also have been searching for a simple script or tool to convert to gff format to use in SNP annotation, I am wanting to convert xml to gff though. If you are working with the human genome you can download from UCSC genome dbSNP in gff format I'm pretty sure, my problem is I am working with the bovine genome! Here is a link to a sequence converter, unfortunately vcf isn't one of the input formats but it may be useful

      Cheers
      Last edited by cow_girl; 03-02-2011, 10:38 AM. Reason: typo

      Comment


      • #4
        If you have vcf file and want to annotate SNP you can use

        1) EnsEMBL Variant effect predictor
        2) snpEff software

        both works with cow, accepts vcf file as input and gives GENEID, transcript ID, protein name.

        Comment


        • #5
          Thanks for the answers!
          I was going to use the UCSC and download a file with SNPs in gtf format but looks like the latest - dbSNP132 has not been added to UCSC yet
          I'll try with the
          1) EnsEMBL Variant effect predictor
          2) snpEff software
          Thanks

          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
          49 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