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