Good day,
When importing a VCF file from VariantAnnotation's data directory into R, a warning is emitted.
library(VariantAnnotation)
aFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", package = "VariantAnnotation")
aSet <- readVcf(aFile, "hg19")
Warning message:
In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Is there some problem with one of the VCF file's format which is distributed with VariantAnnotation ? I wouldn't expect any package data files to emit warnings to the end user.
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10
VariantAnnotation 1.18.7
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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia