Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GATK - dbSNP .rod files

    Hi,

    I am using GATK to adjust my per base quality scores in a .bam file. Does anyone know how to download a dbSNP v132 .rod file in order to exclude already known variants so they are not interpreted as mismatches?

    Also, can anyone recommend covariates to use in the CountCovariates analysis?

    Thanks

    Kath

  • #2
    You can build your own rod file (I've done this with hg19/db131): http://www.broadinstitute.org/gsa/wi.../The_DBSNP_rod

    Comment


    • #3
      Thanks for your response. I had seen the website but found it assumed more informatics knowledge than I possess. For example, it tells you how to merge two rod files but not how to get the rod for dbSNP 132 in the first place...

      Comment


      • #4
        Actually you don't need to have a rod file for dbsnp132:

        http://getsatisfaction.com/gsa/topics/dbsnp132_rod

        d

        Comment


        • #5
          Thanks, I hadn't noticed that thread.
          Kath

          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
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          52 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X