Hi,

Struck an issue with running 'readVcf' function (in VariantAnnotation package) if it is called after genotypeToSnpMatrix(), or importing snpStats package. It works fine if called first. Simple workaround is to import SNPstats before VariantAnnotation - but might be worth a bug report?

Examples below based on the vignette - first with bug:

#--------------------------------------------------------
# Session 1
# vcf1 loads
# vcf2 yeilds error:

library(VariantAnnotation)

# From the doco/sample files
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf1 <- readVcf(fl, "hg19") # vcf1 is ok!

res1 <- genotypeToSnpMatrix(vcf1)
#messages:
#Attaching package: ‘Matrix’
#The following object is masked from ‘package:VariantAnnotation’:
#    expand
#The following object is masked from ‘package:S4Vectors’:
#    expand
#Warning message:
#    In .local(x, ...) : non-single nucleotide variations are set to NA

vcf2 <- readVcf(fl, "hg19")
# Now same command causes error:
#Error: scanVcf: scanVcf: scanTabix: '.SigArgs' is shorter than '.SigLength' says it should be
#path: /my/path/R/x86_64-pc-linux-gnu-library/3.3/VariantAnnotation/extdata/chr22.vcf.gz
#index: /my/path/R/x86_64-pc-linux-gnu-library/3.3/VariantAnnotation/extdata/chr22.vcf.gz.tbi
#path: /my/path/R/x86_64-pc-linux-gnu-library/3.3/VariantAnnotation/extdata/chr22.vcf.gz

And second with workaround:

#--------------------------------------------------------
# Session 2 - works

# Load SNP stats first
library(snpStats)
library(VariantAnnotation)

fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf1 <- readVcf(fl, "hg19") # vcf1 is ok!
res1 <- genotypeToSnpMatrix(vcf1)
#Warning message:
#    In .local(x, ...) : non-single nucleotide variations are set to NA
vcf2 <- readVcf(fl, "hg19")  # vcf2 is ok.

Thanks,

Sarah.

# > sessionInfo()
# R version 3.3.0 (2016-05-03)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 14.04.4 LTS
#
# locale:
#     [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
# [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
# [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
#
# attached base packages:
#     [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
#
# other attached packages:
#     [1] snpStats_1.22.0            Matrix_1.1-2               survival_2.37-7            VariantAnnotation_1.18.7  
# [5] Rsamtools_1.24.0           Biostrings_2.40.2          XVector_0.12.1             SummarizedExperiment_1.2.3
# [9] Biobase_2.20.0             GenomicRanges_1.24.3       GenomeInfoDb_1.8.7         IRanges_2.6.1             
# [13] S4Vectors_0.10.3           BiocGenerics_0.18.0       
#
# loaded via a namespace (and not attached):
#     [1] AnnotationDbi_1.34.4    zlibbioc_1.18.0         GenomicAlignments_1.8.4 BiocParallel_1.6.6      lattice_0.20-24        
# [6] BSgenome_1.40.1         tools_3.3.0             grid_3.3.0              DBI_0.4-1               rtracklayer_1.32.2     
# [11] bitops_1.0-6            RCurl_1.95-4.1          biomaRt_2.18.0          RSQLite_0.11.2          GenomicFeatures_1.24.5
# [16] XML_3.98-1.1