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Signed-off-by: David Spencer <idlemoor@slackbuilds.org> |
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snpEff.SlackBuild |
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