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Ensembl Variation - Variant tools

Ensembl provides several tools related to variant data:

Variant Effect Predictor (VEP)

Determines the effect of your variants on genes, transcripts, and protein sequence, as well as regulatory regions.

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Linkage Disequilibrium Calculator

Calculate Linkage Disequilibrium (LD) between variants using genotypes from a selected population.

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Variant Recoder

Translate a variant identifier or HGVS notation to all possible variant IDs and HGVS

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Haplosaurus

Computes observed transcript haplotype sequences based on phased genotype data

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Variant Simulator

Generate all single base substitutions for protein coding genes given a specific species or chromosome or gene.

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Available as a web tool
Available as a REST API
Available as a Perl standalone script