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Annotate with local reference bases (REF_BASES)

Category Variant Annotations


Local reference context at a variant position.

The annotation gives ten reference bases each to the left and right of the variant start and the start base for a total of 21 reference bases. Start position is defined as one base before indels. For example, the reference context AAAAAAAAAACTTTTTTTTTT would apply to a SNV variant context with ref allele C and alt allele G as well as to a deletion variant context with ref allele CT and alt allele C.

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GATK version built at Wed, 9 Oct 2019 15:19:59 -0400.