I'm seeing an error when I read in a compress vcf, but not when I read in the uncompressed vcf.  Can anyone point me in the right direction to figure out what I'm doing wrong?  I've tried this on 3 different vcfs with the same error (different record fails).

> # read in a complete file
> fl <- "first10K.vcf"
> vcf <- readVcf(fl, "hg19")
> vcf
class: VCF
dim: 9934 998
genome: hg19
exptData(1): header
fixed(4): REF ALT QUAL FILTER
info(39): NS DP ... HD HP
geno(6): GT VR ... GQ FT
rownames(9934): 1:69270 1:69360 ... 1:19597392 1:19597396
rowData values names(1): paramRangeID
colnames(998): A00003 A00057 ... A16457 ''
colData names(1): Samples
>
> # now try again but compress it first
> fl <- "first10K.vcf"
> compressVcf <- bgzip(fl, tempfile())
> idx <- indexTabix(compressVcf, "vcf")
> tab <- TabixFile(compressVcf, idx)
> vcf <- readVcf(tab, "hg19")
Error: scanVcf: record 4370 INFO '0/0:.:130:131:.:.' not found
  path: C:\Users\bdavis2\AppData\Local\Temp\RtmpwrXcST\file1dc84cff4177
>
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] VariantAnnotation_1.2.10 Rsamtools_1.8.6          Biostrings_2.24.1        GenomicRanges_1.8.13
[5] IRanges_1.14.4           BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.18.1  Biobase_2.16.0        biomaRt_2.12.0        bitops_1.0-4.1
 [5] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3 grid_2.15.1
 [9] lattice_0.20-10       Matrix_1.0-9          RCurl_1.95-1.1        RSQLite_0.11.2
[13] rtracklayer_1.16.3    snpStats_1.6.0        splines_2.15.1        stats4_2.15.1
[17] survival_2.36-14      tools_2.15.1          XML_3.95-0.1          zlibbioc_1.2.0

Brian


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