Question: Bioconductor and WGS: recommended practices?
0
gravatar for Vincent J. Carey, Jr.
3 months ago by
United States
Vincent J. Carey, Jr.6.3k wrote:

I searched the support site for references to WGS, and "whole genome sequencing", and nothing came back. One experimental data package called cgdv17 is available that includes excerpts from Complete Genomics public release. This package was apparently made back in 2011. It defines a "raggedVariant" class to handle in a unified way information from VCFs that have variants that are not shared between samples. Since then, VRanges has become available, and seems quite relevant.

Before I work on upgrading cgdv17 to use more current infrastructure such as GenomicFiles, I wanted to check with the community to see if there are approaches to working with WGS data in Bioconductor of which I am unaware.

ADD COMMENTlink written 3 months ago by Vincent J. Carey, Jr.6.3k

Hey Vince, not that I am of. Outside of VCF and R, there is the tab-delimited Mutation Annotation Format (MAF), but I'm not sure it has really caught on. Generally, I think that Bioconductor could benefit from having much more variant / mutation datasets, like:

  • 1000 Genomes, ExAc, etc
  • COSMIC
  • et cetera
ADD REPLYlink written 3 months ago by Kevin Blighe90
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