[BioC] Subsetting vcf file by subject

[Valerie Obenchain]

Hi Margaret,

Currently VariantAnnotation doesn't support subsetting a VCF file by 
subject. We are planning to implement this in the next devel cycle.

Valerie

On 03/25/2013 07:26 AM, Taub, Margaret wrote:
> Hi all,
>
> I am interested in reading in only a subset of the subjects contained in a large multi-sample vcf file. As far as I can see, there is a lot of great functionality in VariantAnnotation for subsetting vcfs based on genomic coordinates, annotation, etc. but I can't see anything for subsetting samples, either in the current release or the devel version. Any help would be greatly appreciated!
>
> Cheers,
> Margaret
>
>
>
> Margaret Taub, PhD
> Assistant Scientist
> Department of Biostatistics
> Johns Hopkins University
> Bloomberg School of Public Health, E3546
> 410-614-9408
> mtaub at jhsph.edu<mailto:mtaub at jhsph.edu>
>
>> sessionInfo()
> R version 2.15.2 Patched (2013-02-08 r61876)
> 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.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] VariantAnnotation_1.4.12 Rsamtools_1.10.2         Biostrings_2.26.3
> [4] GenomicRanges_1.10.6     IRanges_1.16.4           BiocGenerics_0.4.0
> [7] RColorBrewer_1.0-5
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.20.3   Biobase_2.18.0         biomaRt_2.14.0
>   [4] bitops_1.0-5           BSgenome_1.26.1        DBI_0.2-5
>   [7] GenomicFeatures_1.10.1 parallel_2.15.2        RCurl_1.95-3
> [10] RSQLite_0.11.2         rtracklayer_1.18.2     stats4_2.15.2
> [13] tools_2.15.2           XML_3.95-0.1           zlibbioc_1.4.0
>
> 	[[alternative HTML version deleted]]
>
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