Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • annovar output problems

    Hi,

    I have trouble making Annovar’s gene annotation tool work well.

    I am working on a virus, so had to build the reference by myself following Annovar’s website indications. I so build the refGene file, the refLink one, and through Annovar’s retrieve_seq_from_fasta.pl, the fasta file. I then run a vcf file, already passed through the convert2annovar.pl script in order to prepare it correctly for the input, and had as a result every variant listed as “intergenic”.

    I am working on a Mac OSX 10.6.8, but if needed have access to a new Linux environment.
    I tried with both the old version of Annovar and the recently released one (few days ago).

    The script has been called like this:

    /path/.../annotate_variation.pl --geneanno --outfile sample --dbtype refGene --buildver NC_XXXXX sample.annovar /path/.../NC_XXXXX/

    File samples (I’ll just show one line. Notice that the variant I show is exonic):

    refGene.txt file (Reference):

    94 U11 gene NC_XXXXX - 18924 21578 18965 21578 1 18924 21578 . U11 gene unk unk 2

    refMrna.fa file (Reference):

    >U11 gene Comment: this sequence (leftmost exon at NC_XXXXX:18924) is generated by ANNOVAR on Fri Jun 28 12:06:03 2013, based on regions speficied in /Users/Marco/Desktop/NC_XXXXXdb/NC_XXXXX_refGene.txt and sequence files stored at /Users/Marco/Desktop/NC_XXXXXdb.
    ATGGATCTGCAAAGACATCCGATTCCGTTTGCGTGGCTAGATCGAGACAAAGTTGAGCGTCTTACAGATTTTCTCAGCAATTTGGAAAGACTGGATAATGTAGATTTGCGAGAGCATCCCCATGTGACTAA....

    sample.annovar file (input):

    NC_XXXXX 20309 20309 A G hom . 5

    sample.variant_function (OUTPUT):

    intergenic NONE(dist=NONE),NONE(dist=NONE) NC_XXXXX 20309 20309 A G hom . 5

    sample.exonic_variant_function (OUTPUT):

    This file was empty.


    Thanks in advance for the help. If more info are needed, please do not hesitate asking me.

  • #2
    Maybe someone here can help, but in the past I emailed the author of ANNOVAR and he got back to me quickly with help; so if you can't figure it out maybe email him.

    Comment


    • #3
      Yeah, that was my next step, but usually this forum works so well that I prefer to try first here.

      Thanks for the suggestion anyway

      Comment


      • #4
        how to build database in annovar for virus

        Dear Marco,

        I am also working on virus. How did you build the database.

        Can you please guide me in building the database for virus?

        Thanks.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM
        • seqadmin
          Multiomics Techniques Advancing Disease Research
          by seqadmin


          New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

          A major leap in the field has
          ...
          02-08-2024, 06:33 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 02-28-2024, 06:12 AM
        0 responses
        25 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-23-2024, 04:11 PM
        0 responses
        72 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2024, 08:52 AM
        0 responses
        80 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-20-2024, 08:57 AM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Working...
        X