Question: Subsetting vcf file by subject
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gravatar for Valerie Obenchain
5.9 years ago by
United States
Valerie Obenchain6.7k wrote:
Hi Margaret, This has been implemented in VariantAnnotation 1.7.4. You'll also need Rsamtools 1.13.3. fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") param <- ScanVcfParam(samples="NA00002") vcf <- readVcf(fl, "hg19", param=param) > geno(vcf)$GT NA00002 rs6054257 NA 20:17330 "1|0" rs6040355 NA 20:1230237 NA microsat1 "0|1" Valerie On 03/25/2013 08:42 AM, Valerie Obenchain wrote: > 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 >> > > _______________________________________________ > 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
ADD COMMENTlink written 5.9 years ago by Valerie Obenchain6.7k
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