[Blends-commit] r2771 - /projects/med/trunk/debian-med/tasks/bio-ngs

[project2501a-guest at users.alioth.debian.org]

Author: project2501a-guest
Date: Sat Apr 23 19:58:20 2011
New Revision: 2771

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2771
Log:
ADD: ANNOVAR

Modified:
    projects/med/trunk/debian-med/tasks/bio-ngs

Modified: projects/med/trunk/debian-med/tasks/bio-ngs
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-ngs?rev=2771&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Sat Apr 23 19:58:20 2011
@@ -136,3 +136,36 @@
  next-generation sequencing platforms such as Illumina's Genome Analyzer II. 
  The algorithm uses a Bayesian framework to improve the quality of the reads 
  in a given data set by employing maximum a posteriori estimation.
+
+Depends: ANNOVAR
+Homepage: http://www.openbioinformatics.org/annovar/
+License: Open Source for non-profit
+ ANNOVAR is an efficient software tool to utilize update-to-date information 
+ to functionally annotate genetic variants detected from diverse genomes 
+ (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and 
+ many others). Given a list of variants with chromosome, start position, end 
+ position, reference nucleotide and observed nucleotides, ANNOVAR can perform:
+ 1) Gene-based annotation: identify whether SNPs or CNVs cause protein coding 
+ changes and the amino acids that are affected. Users can flexibly use RefSeq 
+ genes, UCSC genes, ENSEMBL genes, GENCODE genes, or many other gene definition
+ systems.
+ 2) Region-based annotations: identify variants in specific genomic regions, 
+ for example, conserved regions among 44 species, predicted transcription
+ factor binding sites, segmental duplication regions, GWAS hits, database
+ of genomic variants, DNAse I hypersensitivity sites, ENCODE 
+ H3K4Me1/H3K4Me3/H3K27Ac/CTCF sites, ChIP-Seq peaks, RNA-Seq peaks, or many
+ other annotations on genomic intervals. 
+ 3) Filter-based annotation: identify variants that are reported in dbSNP, 
+ or identify the subset of common SNPs (MAF>1%) in the 1000 Genome Project,
+ or identify subset of non-synonymous SNPs with SIFT score>0.05, or many 
+ other annotations on specific mutations.
+ 4) Other functionalities: Retrieve the nucleotide sequence in any 
+ user-specific genomic positions in batch, identify a candidate gene list 
+ for Mendelian diseases from exome data, identify a list of SNPs from 
+ 1000 Genomes that are in strong LD with a GWAS hit, and many other 
+ creative utilities. 
+ In a modern desktop computer (3GHz Intel Xeon CPU, 8Gb memory), for 
+ 4.7 million variants, ANNOVAR requires ~4 minutes to perform 
+ gene-based functional annotation, or ~15 minutes to perform stepwise 
+ "variants reduction" procedure, making it practical to handle hundreds 
+ of human genomes in a day.