I have a VCF created by Bis-SNP. One of the INFO fields is called CS but readVcf is ignoring it and I can't figure out why. A tiny example VCF can be downloaded from https://www.dropbox.com/sh/bmbyjgts26req8k/AAA4UkTTUU8IzNxkcy4ZP14Ua?dl=0 that can be used to reproduce the problem.

This is what I've tried:

> library(VariantAnnotation)
> x <- readVcf('~/tmp/ex.vcf.gz', 'hg19')

# Missing CS field. Should appear before Context.
> info(x)
DataFrame with 2 rows and 9 columns
                       Context        DB        DP        HQ       MQ0        NS        QD             REF        SB
               <CharacterList> <logical> <integer> <numeric> <integer> <integer> <numeric> <CharacterList> <numeric>
rs55998931                  YH      TRUE         8        NA         0         1        NA              CH   -0.1412
chr1:10774_G/C              SG     FALSE         4        NA         0         1        NA              CH   -0.6254

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] VariantAnnotation_1.12.2 Rsamtools_1.18.1         Biostrings_2.34.0        XVector_0.6.0            GenomicRanges_1.18.1    
[6] GenomeInfoDb_1.2.2       IRanges_2.0.0            S4Vectors_0.4.0          BiocGenerics_0.12.0     

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1    base64enc_0.1-2         BatchJobs_1.4           BBmisc_1.7              Biobase_2.26.0         
 [6] BiocParallel_1.0.0      biomaRt_2.22.0          bitops_1.0-6            brew_1.0-6              BSgenome_1.34.0        
[11] checkmate_1.5.0         codetools_0.2-9         DBI_0.3.1               digest_0.6.4            fail_1.2               
[16] foreach_1.4.2           GenomicAlignments_1.2.0 GenomicFeatures_1.18.2  iterators_1.0.7         RCurl_1.95-4.3         
[21] RSQLite_1.0.0           rtracklayer_1.26.1      sendmailR_1.2-1         stringr_0.6.2           tools_3.1.1            
[26] XML_3.98-1.1            zlibbioc_1.12.0   

Thanks for your help,

Pete

Now fixed in release (1.12.3) and devel (1.13.5).