[BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'

[Julian Gehring]

Hi,

Is there a direct way to specifiy the 'seqinfo' of a genome for the 
import of a VCF file using 'readVcf'?  I'm aware that one can change it 
with the 'seqinfo' method afterwards, but for large VCF files this can 
take a significant amount of time.

An alternative would be to sneak it in by the 'which' arguments, such as:

readVcf(file, genome, ScanVcfParam(which = as(seq_info, "GRanges")))

but this requires the file to be indexed beforehand.

Best wishes
Julian