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@jhsph.edu<mailto:mtaub@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

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