Using the Bioconductor VariantAnnotation Package to Annotate Genetic Variants
The VariantAnnotation package has facilities for reading in all or portions of Variant Call Format (VCF) files. Structural location information can be determined as well as amino acid coding changes for non-synonymous variants. Consequences of the coding changes can be investigated with the SIFT and PolyPhen database packages.
The vignette outlines a general workflow for annotating and filtering genetic variants using the VariantAnnotationpackage. Sample data are in VariantCall Format (VCF) and are a subset of chromosome 22 from 1000 Genomes. VCF is a text file format that contains meta-information lines, a header line with column names, data lines with information about a position in the genome, and optional genotype information on samples for each position. A full description of the VCF format can be found on the 1000 Genomes page, http://www.1000genomes.org/. Sample data are read in from a VCF file and variants are identified according to region such as coding, intron, intergenic, spliceSite etc. Amino acid coding changes are computed for the non-synonymous variants and SIFT and PolyPhen databases provide predictions of how severely the coding changes affect protein function. The end of the vignette covers other transformations of VCF data such as the creation of a SnpMatrix or a long form GRanges.
it's potentially useful, I guess that you're posting all these variant annotation tools, but, as someone who intends to look into these more, what I'd find actually useful is if you had a single post containing a commentary on these options. It could give a small snippet on usage, or your personal experience with each, or a summary of when to use what. That would be helpful for me anyway....
also that would probably be best to be posted in the tutorial section. I do plan to do something similar for a number of tools as a compendium to a course that I am teaching this Fall
My understanding was that the tools section is generally for descriptions of individual tools... I will add comments on individual tools as I go, but my hope was that by adding them here, the community would collectively add these comments, and vote for those they like. After a few hours we can already start to get a crude sense which are more popular than others based on votes, one of the developers of VAAST gives us the heads up about a new version coming soon, etc.
Perhaps the tools section should have a sticky post explaining when/how to use the tools section and what the ideal features of a tool post might be. My own opinion is that each tool new or old has one post, info on new versions can be added to the post as needed, the answers and comments of this post can be used for general commentary on where the tool is useful or not, general impressions, etc. General questions about what the tool is about might be added as comments but specific questions or problems with the tool should be submitted as an independent question post.
yes the tool section was originally intended mostly an announcement with a small description then other posts would be used to compare them or discuss various features.
Great, I'm interested to see your comments.