[Bioc-devel] VariantAnnotation: Same locus, multiple samples
Julian Gehring
julian.gehring at embl.de
Fri Dec 5 10:18:35 CET 2014
Hi,
Assume that we have two variants from two samples at the same locus,
stored in a 'VRanges' or 'VCF' object:
library(VariantAnnotation)
vr = VRanges("1", IRanges(c(10, 10), width = 1),
ref = c("C", "C"), alt = c("A", "G"),
sampleNames = c("S1", "S2"))
vcf = as(vr, "VCF")
If we convert the VCF to a VRanges, we now get each variant in each
patient:
vr2 = as(vcf, "VRanges")
length(vr) ## 2
length(vr2) ## 4
It seems that the VCF object does not store the information of the
'sampleNames' in the first conversion.
Best wishes
Julian
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