mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-22 19:44:21 +01:00
28 lines
1.4 KiB
Text
28 lines
1.4 KiB
Text
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
|