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diff --git a/academic/snpEff/README b/academic/snpEff/README new file mode 100644 index 0000000000..a32c83dfba --- /dev/null +++ b/academic/snpEff/README @@ -0,0 +1,28 @@ +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 |