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 [[alternative HTML version deleted]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >