academic/snpEff: Added (Genes toolbox).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 28 insertions, 0 deletions

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+SnpEff: Genetic variant annotation and effect prediction toolbox
+
+SnpEff is a variant annotation and effect prediction tool. It
+annotates and predicts the effects of variants on genes (such as amino
+acid changes).
+
+Input: The inputs are predicted variants (SNPs, insertions, deletions
+and MNPs). The input file is usually obtained as a result of a
+sequencing experiment, and it is usually in variant call format (VCF).
+
+Output: SnpEff analyzes the input variants. It annotates the variants
+and calculates the effects they produce on known genes (e.g. amino
+acid changes).
+
+This also installs SnpSift, a toolbox that allows you to filter and
+manipulate annotated files. Once your genomic variants have been
+annotated, you need to filter them out in order to find the 
+"interesting / relevant variants". Given the large data files, this is
+not a trivial task (e.g. you cannot load all the variants into XLS
+spreadsheet). SnpSift helps to perform this VCF file manipulation and
+filtering required at this stage in data processing pipelines. 
+
+If you are using SnpEff or SnpSift, please cite:
+A program for annotating and predicting the effects of single
+nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
+melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang
+le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin).
+2012 Apr-Jun;6(2):80-92. PMID: 22728672