library(Rsamtools)
bcf <- BcfFile("subset.bcf",mode="rb")
open(bcf)

region <- GRanges(seqnames=c("scaffold_1"), ranges=IRanges(start=c(0,500),end=c(400,10000)), strand="+")
params <- ScanBcfParam(which=region)
scanBcf(bcf,param=params)