Is random access by row index possible for an indexed VCF file?
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maltethodberg ▴ 180
@maltethodberg-9690
Last seen 8 hours ago
Denmark

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.

Rsamtools VariantAnnotation • 413 views
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@james-w-macdonald-5106
Last seen 10 hours ago
United States

No, the tabix file that is used for random access is based on genomic regions, not rows of the VCF file.

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