Entering edit mode
Is it possible to import specific rows from an indexed VCF file with VariationAnnotation, without manually specifying the ranges?
I would simply like to do the following:
# Dummy file
library(VariantAnnotation)
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
# This read the entire matrix:
readGeno(fl, x="GT")
# Desired output is this, but without reading in the entire matrix in first:
readGeno(fl, x="GT")[c(1,3,5),]
I realise you can specify a ScanVcfParam
argument, but that only takes ranges as input, and not rows directly.