I just quickly wrote a set of Tools to annotate my VCFs ( http://plindenbaum.blogspot.fr/2013/02/4-tools-i-wrote-today-to-annotate-vcf.html )
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 ?