[BioC] readVcf bgzip error

[Valerie Obenchain]

Hi Brian,

I'm not sure what's going on here. Can you point me to where you got 
this file or is it small enough to send?

Valerie




On 10/09/2012 12:06 PM, Davis, Brian wrote:
> 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
>
>
> 	[[alternative HTML version deleted]]
>
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