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