SnpEff¶

Description¶

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). Typical usage : 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). A list of effects and annotations that SnpEff can calculate can be found here.

Environment Modules¶

Run module spider snpeff to find out what environment modules are available for this application.

Environment Variables¶

HPC_SNPEFF_DIR - installation directory
HPC_SNPEFF_BIN - executable directory
HPC_SNPEFF_CONF - configuration file directory
HPC_SNPEFF_EX - examples directory

Categories¶

biology, annotation