Decipher the effect of SNPs

Description

Several softwares can be used:

  • Variant Effect Predictor (VEP from EBI)
  • SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

In this example, we use SnpEff.

Data types

Inputs

SNP discovery VCF file and Genome annotation GFF3 file.

Output

Enriched VCF file with the SNP effect on genes.

Challenges

Choose the same reference sequence and select the proper amino acid code.

Recommendation

Use the wheat survey sequence as the reference sequence for the moment. When the complete wheat genome is sequenced (in 3 years at the earliest), it make it possible to remap the SNPs on the new reference.

Select VCF as output format.

 

Writing: Michael Alaux, Nacer Mohellibi, Loic Couderc

Creation date: 02 October 2014

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