AnnotateVcf-CellBaseR-method: AnnotateVcf
In cellbaseR: Querying annotation data from the high performance Cellbase web

Description Usage Arguments Value See Also Examples

This method is a convience method to annotate bgzipped tabix-indexed vcf files. It should be ideal for annotating small to medium sized vcf files.

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## S4 method for signature 'CellBaseR'
AnnotateVcf(object, file, batch_size, num_threads,
  BPPARAM = bpparam())

`object`	an object of class CellBaseR
`file`	Path to a bgzipped and tabix indexed vcf file
`batch_size`	intger if multiple queries are raised by a single method call, e.g. getting annotation info for several genes, queries will be sent to the server in batches. This slot indicates the size of each batch, e.g. 200
`num_threads`	number of asynchronus batches to be sent to the server
`BPPARAM`	a BiocParallel class object

a dataframe with the results of the query

https://github.com/opencb/cellbase/wiki and the RESTful API documentation http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/

cb <- CellBaseR()
fl <- system.file("extdata", "hapmap_exome_chr22_200.vcf.gz",
                  package = "cellbaseR" )
res <- AnnotateVcf(object=cb, file=fl, BPPARAM = bpparam(workers=2),batch_size=100)