For the following line

    vr = readVcfAsVRanges(paste0("Data/", vcf.file), "human_g1k_v37")

I get warning message:

Warning messages:
1: In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames

Could any one please explain to me what this means?

The last line in header:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  HEI0046N    HEI0046T

Some other part that might be called key:

##contig=<ID=chr1,length=249250621>
##contig=<ID=chr1_gl000191_random,length=106433>
##contig=<ID=chr1_gl000192_random,length=547496>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr4_gl000193_random,length=189789>
##contig=<ID=chr4_gl000194_random,length=191469>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>

I do not see duplications.

It definitely comes from the 'header' lines (before the #CHROM... line in your VCF file); after running

example(scanVcfHeader)
hdr = scanVcfHeader(fl)

one could examine each field

info(hdr)

etc., looking for a data frame with row names that have been made unique (with an artificial '.1' added to the end). My guess would be an element of meta(hdr), which could safely be ignored (on the other hand, one might want to correct a duplicate info(hdr) field).