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SNP annotation

I have a list of SNPs and InDels generated using BWA-GATK in VCF format from bacteria genome. How do I carry SNP annotation if I can not find SNP database for bacteria? Do you recommand using GATK VariantAnnotator for bacteria samples as there is no SNP database?
What is the best and easy way of annotating SNPs/InDels if reference genome of the organism is not available?

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I'm sorry, I don't understand your question. Can you please clarify what you are trying to do and what you mean by "SNP annotation"? Also, please note that if there is no reference genome for your organism, you will not be able to use the GATK. All GATK tools require a reference file to be able to work.

  • redred Member

    Can you please explain the benefit using GATK VariantAnnotator tool for bacteria sample?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Please see the documentation for a description of the function of the VariantAnnotator tool.

    If you have any specific questions about how to use it, or if you run into problems while using it, I will be happy to answer your questions. But I do not have the time nor the inclination to re-explain what is the function of each tool, when that is already described in the documentation.

  • redred Member

    I am sorry that my question was not clear, my question was a follow up from the previous question. I want to use the tool for haploid sample rather than a diploid sample. The databases (dbSNP) is for diploid. So I was just asking if VariantAnnotator tool can be used for bacteria sample.

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