Using the GATK API to annotate my VCF
Posted in Ask the GATK team | Last updated on

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I just quickly wrote a set of Tools to annotate my VCFs ( )

For example, one of those tools uses a BED/XML file indexed with tabix to annotate my VCF . (My code just uses the java api for tabix to get the XML at a given position)

Question: is there something in the GATK-API that would allow me to implement my code using the GATK-API: What kind of walker should I use ? What would be the benefits of using the GATK-API ? for example does using a gatk-walker will automatically make my code parallelizable ?


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