[Blends-commit] [SCM] med branch, master, updated. d9477063ad098eb6a9214b4f71c50ada58a99b13

[Steffen Moeller]

The following commit has been merged in the master branch:
commit d9477063ad098eb6a9214b4f71c50ada58a99b13
Author: Steffen Moeller <moeller at debian.org>
Date:   Mon Sep 25 11:05:32 2017 +0200

    task bio-ngs true part of bio

diff --git a/tasks/bio b/tasks/bio
index 2db34a7..76fc631 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -112,6 +112,10 @@ Recommends: last-align, maq, ssake, velvet | velvet-long
 
 Recommends: qiime
 
+Recommends: scoary
+
+Recommends: umap
+
 X-End-Category: high-throughput sequencing
 
 X-Begin-Category: Analysis of RNA sequences.
@@ -214,6 +218,8 @@ Recommends: samtools, bedtools, filo, datamash
 
 Recommends: gassst
 
+Recommends: hinge
+
 Recommends: r-bioc-hilbertvis
 Remark: It would be interesting to package HilbertVisGUI (see below) as well.
 
@@ -2892,6 +2898,42 @@ Pkg-Description: family of gene prediction programs
  A family of gene prediction programs developed at Georgia Institute of
  Technology, Atlanta, Georgia, USA.
 
+Recommends: annovar
+Homepage: http://www.openbioinformatics.org/annovar/
+License: Open Source for non-profit
+Pkg-Description: annotate genetic variants detected from diverse genomes
+ 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.
+
 Recommends: python-orange
 License: GPLv3
 Homepage: http://orange.biolab.si/

-- 
Debian Med metapackages