Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Is there a tool that converts TXT, BED, GFF format to VCF?

    Hi,

    I would like to ask if there is tool out there that would convert variants in a certain file format (such as .txt, .gff, .bed) to VCF format?

    Thank you for your help.
    Laura

  • #2
    PacBio's SMRT suite has a python script to supposedly go from GFFv4 to VCF.

    But, I recall on the BEDTools discussion board, Aaron Quinlan has mentioned that going from GFF or BED to VCF is not a simple task, unless the input files were originally created to track all the information required for the VCF output. That makes it difficult to write generic scripts for conversion.
    Michael Black, Ph.D.
    ScitoVation LLC. RTP, N.C.

    Comment


    • #3
      Originally posted by mbblack View Post
      PacBio's SMRT suite has a python script to supposedly go from GFFv4 to VCF.
      Was that a typo? Did you mean GFF v3 perhaps?

      Comment


      • #4
        Originally posted by maubp View Post
        Was that a typo? Did you mean GFF v3 perhaps?
        I was just glancing at their website, but I think it means their script is v.4 (or the entire SMRT suite is v.4), not that they've created their own GFF version!

        Analysis workflows and tools for WGS, targeted, RNA, epigenetics and microbiome and metagenomic sequencing for advanced users.
        Last edited by mbblack; 12-05-2011, 12:35 PM.
        Michael Black, Ph.D.
        ScitoVation LLC. RTP, N.C.

        Comment


        • #5
          In my hands, the VCF v3.3 (exotic version if one with weird call syntax for the ALT field) format produced by SMRTv4 accompanying gffToVcf (v3.0 - pbgenomicconsensus) is not conform to the VCF4 specs and when used with VCF compatible tools, leads to errors.

          Here an example from a very simple run
          <pre>
          ##fileformat=VCFv3.3
          ##fileDate=2017121
          ##source=gffToVcf --resolved-tool-contract /opt/pacbio/userdata/jobs_root/000/000096/tasks/genomic_consensus.tasks.gff2vcf-0/resolved-tool-contract.json
          ##INFO=NS,1,Integer,"Number of Samples with Data"
          ##INFO=DP,1,Integer,"Total Depth of Coverage"
          #CHROM POS ID REF ALT QUAL FILTER INFO
          chromosome_2 486515 . C T 93.00 0 NS=1;DP=47
          chromosome_2 487451 . C D1 93.00 0 NS=1;DP=47
          chromosome_2 511331 . . IA 41.00 0 NS=1;DP=52
          chromosome_2 537571 . . IA 55.00 0 NS=1;DP=40
          chromosome_2 636693 . A G 93.00 0 NS=1;DP=31
          chromosome_2 643391 . G T 93.00 0 NS=1;DP=46
          chromosome_2 643959 . A D1 93.00 0 NS=1;DP=50
          </pre>

          Before I adventure in this, does anyone have a GFF3 to VCF4 converter that works on Sequel data?
          Fields required to make a VCF from their GFF3 are there, it is 'only' a matter of operating a smart conversion between the two tabular formats and fixing coordinate issues and alternate allele cases (if present?!).
          Thanks
          http://www.bits.vib.be/index.php

          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
          8 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          8 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
          66 views
          0 likes
          Last Post seqadmin  
          Working...
          X