[Bioc-devel] Warning when Reading Example VCF

Dario Strbenac dstr7320 at uni.sydney.edu.au
Tue Sep 27 10:00:03 CEST 2016

Good day,

When importing a VCF file from VariantAnnotation's data directory into R, a warning is emitted.

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

Dario Strbenac
University of Sydney
Camperdown NSW 2050

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