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Test-drive the GATK tools and Best Practices pipelines on Terra
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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?