is part of this an issue with the VCF format itself?

http://campagnelab.org/evaluating-goby-against-the-1000-genome-genotype-calls-and-why-is-vcf-so-inefficient/

or is that a separate concern?

thanks,

--t


On Tue, Oct 23, 2012 at 7:30 PM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> Hi Peter,
>
> I'd say yes, the warning is a cause for concern. Is the vcf you're working
> with publicly available?  If not, can you send a smaller subset that still
> produces the error?
>
> Valerie
>
>
>
> On 10/23/12 17:29, hickey@wehi.EDU.AU wrote:
>
>> I am using the writeVcf() function in the VariantAnnotation package,
>> which I understand to be 'under construction' from the documentation. I am
>> wondering why writeVcf() is taking so long to do it's job and if there is
>> anything I can do to speed this up? For example, I have a VCF object
>> containing some 36,000 variants that I want to write to file and this takes
>> nearly 3 hours. It also produces a warning that I am unsure how to
>> interpret, i.e. should I be worried by it? The VCF written to disk appears
>> to be valid.
>>
>> Many thanks for your help.
>>
>> ## Code
>>
>>> library(VariantAnnotation)
>>> vcf<- readVcf(file = 'UnifiedGenotyper.autosomal.**snps.indels.vcf.gz',
>>> genome = 'mm9')
>>> vcf
>>>
>> class: VCF
>> dim: 292155 7
>> genome: mm9
>> exptData(1): header
>> fixed(4): REF ALT QUAL FILTER
>> info(21): AC AF ... SB STR
>> geno(5): AD DP GQ GT PL
>> rownames(292155): chr1:3003110 chr1:3012398 ... chr19:61340696
>>    chr19:61340708
>> rowData values names(1): paramRangeID
>> colnames(7): 506/Bcl2#292 506/Bcl2#306 ... 506/Bcl2#385 506/Bcl2#409
>> colData names(1): Samples
>>
>> ## Some subsetting of the 'vcf' object to create vcf.2aff.constrained
>>
>>  vcf.2aff.constrained
>>>
>> class: VCF
>> dim: 35514 7
>> genome: mm9
>> exptData(1): header
>> fixed(4): REF ALT QUAL FILTER
>> info(21): AC AF ... SB STR
>> geno(5): AD DP GQ GT PL
>> rownames(35514): chr1:3087036 chr1:3183065 ... chr19:61340449
>>    chr19:61340453
>> rowData values names(1): paramRangeID
>> colnames(7): 506/Bcl2#292 506/Bcl2#306 ... 506/Bcl2#385 506/Bcl2#409
>> colData names(1): Samples
>>
>>  system.time(writeVcf(obj = vcf.2aff.constrained, filename =
>>> 'UnifiedGenotyper.autosomal.**snps.indels.constrained.**
>>> genotypes.2aff.vcf'))
>>>
>>       user    system   elapsed
>> 10653.768     0.244 10659.163
>> Warning message:
>> In .Method(..., deparse.level = deparse.level) :
>>    number of rows of result is not a multiple of vector length (arg 1)
>>
>>  sessionInfo()
>>>
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] VariantAnnotation_1.4.1 Rsamtools_1.10.1        Biostrings_2.26.2
>> [4] GenomicRanges_1.10.2    IRanges_1.16.2          BiocGenerics_0.4.0
>>
>> loaded via a namespace (and not attached):
>>   [1] AnnotationDbi_1.20.1   Biobase_2.18.0         biomaRt_2.14.0
>>   [4] bitops_1.0-4.1         BSgenome_1.26.1        DBI_0.2-5
>>   [7] GenomicFeatures_1.10.0 parallel_2.15.1        RCurl_1.95-1.1
>> [10] RSQLite_0.11.2         rtracklayer_1.18.0     stats4_2.15.1
>> [13] tools_2.15.1           XML_3.95-0.1           zlibbioc_1.4.0
>>
>> ------------------------------**--
>> Peter Hickey,
>> PhD Student/Research Assistant,
>> Bioinformatics Division,
>> Walter and Eliza Hall Institute of Medical Research,
>> 1G Royal Parade, Parkville, Vic 3052, Australia.
>> Ph: +613 9345 2324
>>
>> hickey@wehi.edu.au
>> http://www.wehi.edu.au
>>
>>
>> ______________________________**______________________________**
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>>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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