[BioC] Error when try VariantAnnotation filterVcf vignette example

[Paul Shannon]

Hi Ying,

The difficulty you encountered is natural, and that part of the vignette is misleading.   Thanks for reporting this.  I will make the proper amendments to the vignette.  Sorry to have created the confusion.

Section 3 of the filterVcf vignette demonstrates how to select a small genomic region from a large vcf file -- but we do not provide that vcf file with the package, simply because it is so big.   This section should be marked very clearly with that warning.  

If you do want to reproduce exactly what we is written in that vignette, the file "somaticVcfBeta-HCC1187-H-200-37-ASM-T1-N1.vcf.gz" is available from Complete Genomics Inc:

    http://www.completegenomics.com/public-data/

Truly executable (and reliable!) code starts in section 4.1 of the vignette.  The code that caused you problems demonstrates how to extract a small file which IS included with the package, and is used in section 4 and after.

Thanks for the bug report.   Let me know if you have any further questions.

 - Paul



On Apr 11, 2013, at 8:28 PM, Valerie Obenchain wrote:

> Subject: [BioC] Error when try VariantAnnotation filterVcf vignette example
> Date: Thu, 11 Apr 2013 14:06:26 -0400
> From: ying chen <ying_chen at live.com>
> To: bioconductor at r-project.org <bioconductor at r-project.org>
> 
> 
> 
> Hi guys,
> 
> 
> 
> I tried to run
> the Filter by Genomic Region example on VariantAnnotation package's filterVcf
> vignette page 3, but I kept getting the error message:
> 
> 
> 
>> 
> library(VariantAnnotation)
> 
>> file.gz <- "somaticVcfBeta-HCC1187-H-200-37-ASM-T1-N1.vcf.gz"
> 
>> stopifnot(file.exists(file.gz))
> 
>> file.gz.tbi <- paste(file.gz, ".tbi", sep="")
> 
>> 
> file.gz.tbi
> 
> [1]
> "somaticVcfBeta-HCC1187-H-200-37-ASM-T1-N1.vcf.gz.tbi"
> 
>> 
> file.exists(file.gz.tbi)
> 
> [1] FALSE
> 
>> if(!(file.exists(file.gz.tbi))
> 
> +
> indexTabix(file.gz, format="vcf")
> 
> Error: unexpected symbol in:
> 
> "if(!(file.exists(file.gz.tbi))
> 
>           indexTabix"
> 
> 
> 
> What did I do
> wrong?
> 
> 
> 
> Thanks a lot
> for the help!
> 
> 
> 
> Ying
> 
> 
> 
>> sessionInfo()
> 
> R version 3.0.0 (2013-04-03)
> 
> Platform: x86_64-w64-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] parallel
> stats     graphics  grDevices utils     datasets
> methods   base
> 
> 
> 
> other attached packages:
> 
> [1] VariantAnnotation_1.6.1 Rsamtools_1.12.0        Biostrings_2.28.0
> 
> [4] GenomicRanges_1.12.1
> IRanges_1.18.0
> BiocGenerics_0.6.0
> 
> 
> 
> loaded via a namespace (and not attached):
> 
> [1]
> AnnotationDbi_1.22.1
> Biobase_2.20.0
> biomaRt_2.16.0
> 
> [4] bitops_1.0-5           BSgenome_1.28.0        DBI_0.2-5
> 
> [7]
> GenomicFeatures_1.12.0 RCurl_1.95-4.1
> RSQLite_0.11.2
> 
> [10] rtracklayer_1.20.0
> stats4_3.0.0           tools_3.0.0
> 
> [13] XML_3.96-1.1
> zlibbioc_1.6.0
> 
>> 
> 
> 
> 
> 
> 		 	   		
> 	[[alternative HTML version deleted]]
> 
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