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  • baika
    Member
    • Apr 2012
    • 12
    #1

    SNP annotation

    Hi
    What is the best and easy way of annotating SNPs/InDels if reference genome of the organism is not available through UCSC genome browser? I have a list of SNPs and InDels generated using BWA-GATK in VCF format from the bacteria Staphylococcus aureus. I am trying to annotate them (location of these SNPs in context of reference genome) using ANNOVAR. I have converted this VCF file into the annovar format using convert2annovar.pl option, and it looks fine.

    In order to make my own annotation database I created gff3 file of the reference genome (GenBank file) using bp_genbank2gff3.pl BioPerl script and also validated it using an online gff3 validator available at http://modencode.oicr.on.ca/cgi-bin/...te_gff3_online. The gff3 file looks perfect. Please suggest how to use this gff file for annotation in ANNOVAR.

    Thanks
    Tags: bioinformactics
  • sytiger
    Junior Member
    • May 2013
    • 3
    #2
    I would like to know too.

    Any one could give a hint?

    Thanks

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