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  • Dongliang Ge
    Member
    • Nov 2009
    • 21

    SequenceVariantAnalyzer: analyzing genetic variants from next-gen sequencing

    Friends,

    If you are working on next-generation sequencing studies, particularly if you are interested in annotating, visualizing SNPs, INDELs, CNVs, and identifying genetic variants responsible for biological traits or diseases, please check out our software tool SequenceVariantAnalyzer (SVA):




    SVA is designed for two specific aims:
    1. To annotate the biological functions of the identified genetic variants, organize and visualize them;
    2. To help find the genetic variants that are associated with or responsible for the biological traits or medical outcomes of interest.


    The SVA release package comes with an example project extracted from 10 genomes - 5 cases and 5 controls. To reduce the size of the release package, I release only the data on chromosome X. The web page below shows that you can play with SVA and an example project to "identify (again )" the Factor VIII (F8) gene for type A hemophilia:



    SVA is also featured with an integrated genome browser to help an investigator to explore the user-generated data and data from public domains. Here is a screenshot:



    Particularly, SVA genome browser allows you to conveniently 'introduce' key variants that you identified to compare and see the difference they could make.

    Please give it a try and let us know what you think.

    Lastly, I hope you may find this tool helpful for your next-generation discovery!

    Best regards,

    Dongliang Ge,
    Duke University, USA


    Last edited by Dongliang Ge; 03-04-2010, 02:26 PM.
  • Dongliang Ge
    Member
    • Nov 2009
    • 21

    #2
    SVA is just released!

    Check it out at: http://www.svaproject.org/
    Last edited by Dongliang Ge; 03-01-2010, 09:00 AM.

    Comment

    • Dongliang Ge
      Member
      • Nov 2009
      • 21

      #3
      Its wiki page:

      Comment

      • NGSfan
        Senior Member
        • Apr 2009
        • 181

        #4
        Thanks! Looks interesting! I will have a try with it.

        Comment

        • Dongliang Ge
          Member
          • Nov 2009
          • 21

          #5
          SVA comes with two editions:
          1. Standard edition : ~2.2 Gb. This edition has full annotation functions.
          2. Lite Evaluation edition: ~ 250Mb. This edition does not have annotation function, but can be used to load an example project for evaluation purposes.

          Both editions are free for use.

          Comment

          • mengmarmal
            Junior Member
            • Oct 2009
            • 1

            #6
            Thanks! I will try with it for my dataset.

            Comment

            • wuhoucdc
              Member
              • Oct 2009
              • 14

              #7
              Thanks a lot for the good package, Dongliang. I'll try it in my data.

              Comment

              • Dongliang Ge
                Member
                • Nov 2009
                • 21

                #8
                SVA now comes on a DVD.

                Comment

                • Dongliang Ge
                  Member
                  • Nov 2009
                  • 21

                  #9
                  The website of SVA is now up:

                  Comment

                  • roadrunner
                    Junior Member
                    • Mar 2010
                    • 1

                    #10
                    Hey dongliang nice seeing you here...

                    Comment

                    • Dongliang Ge
                      Member
                      • Nov 2009
                      • 21

                      #11
                      Friends,

                      A lite evaluation edition is released for Windows. Play with it on your laptop!



                      I would also take this chance to thank all the users and their comments!

                      Here I have a screenshot on a Dell E6400 laptop with 32-bit Windows XP:




                      Larger version:

                      Last edited by Dongliang Ge; 03-08-2010, 08:15 AM.

                      Comment

                      • Dongliang Ge
                        Member
                        • Nov 2009
                        • 21

                        #12
                        Causal variants for metachondromatosis are identified.

                        Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

                        Sobreira NLM, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, et al. (2010) PLoS Genet 6(6): e1000991. doi:10.1371/journal.pgen.1000991






                        Comment

                        • Berlinq
                          Junior Member
                          • Dec 2009
                          • 7

                          #13
                          Dear Dongliang
                          Trying, still not working. My input files (SNV and INDEL) look ok, as described in the manual, get an error - please see attachments (also gsap file as a txt)
                          Second problem is that after updating to version 1.02 the programm is asking for CNV tagging data file, Venter's SNP and INDEL files wich are missing in the package.. Where do I get it from?
                          kind regards
                          Attached Files
                          Last edited by Berlinq; 04-05-2011, 01:22 AM.

                          Comment

                          • Dongliang Ge
                            Member
                            • Nov 2009
                            • 21

                            #14
                            Hi Berlinq,

                            Thanks for the message.

                            In your .gsap script file, please change the indel file name extension to .samtoolsindels. That is,

                            [INDELINPUT]=cacoind,/project/erasys1/ngs/sva/svacaco/caindel.samtoolsindels

                            In addition, there is a new SVA version version 1.1 available now. In the new version, the newer vcf format, instead of the older samtools pileup format (the .samtools and .samtoolsindels files), are supported.

                            Best,
                            Dongliang


                            Originally posted by Berlinq View Post
                            Dear Dongliang
                            Trying, still not working. My input files (SNV and INDEL) look ok, as described in the manual, get an error - please see attachments (also gsap file as a txt)
                            Second problem is that after updating to version 1.02 the programm is asking for CNV tagging data file, Venter's SNP and INDEL files wich are missing in the package.. Where do I get it from?
                            kind regards

                            Comment

                            • honey
                              Senior Member
                              • Feb 2010
                              • 151

                              #15
                              Dongling,
                              Will SVA provide quantitative estimation of reads in mutated regoin? IS it mainly for SNPs or it can also detect rearrangement please?

                              Comment

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