Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Can you read VCF.idx?

    Is there a way to use VFC.idx file (other than for viewing)?

    I have a large (42 Gig) VCF and associated VCF.idx - both generated by GATK. I have some simple questions about this VCF like how many variants are in it? How many of them are on CHR1, 2, ... etc? Is there a particular variant (KRAS G13D) in this VCF?

    Is there some way to answer these questions without having to open it in IGV? Clearly this data exists within the idx file. Right?
    Kamalakar Gulukota,
    Director,
    Center for Bioinformatics and Computational Biology
    NorthShore University Health System, [email protected]

  • #2
    I don't know why you think this information would exist in the index file. The index is just used to be able to calculate where in a file to move to extract some desired data. If you want to get various metrics about a VCF file, then just write a program to calculate it (unless one already exists that does exactly what you want).

    Comment


    • #3
      Right. That's what I was afraid of. And I did write some scripts for things I need.

      But, when the file is so large everything takes time and I was hoping that some info in an index file can be used to speed it up.

      The question remains though: What is the structure of the idx file? What information does it have?
      Kamalakar Gulukota,
      Director,
      Center for Bioinformatics and Computational Biology
      NorthShore University Health System, [email protected]

      Comment


      • #4
        You might still be able to use the index if you have a question that needs random file access. If, for example, you wanted to know about a particular stretch of the genome, you could use the index to randomly extract just that part of the VCF file. I believe that the index is a tabix index, so you can have a look at tabix for a C interface, if that's what you want. Alternatively, you could probably use tabix in a script from the command line, though I've never personally tried that.

        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