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Table 1 Methods to characterize SNPs across coding and non-coding regions

From: Innovative strategies for annotating the “relationSNP” between variants and molecular phenotypes

Methodology Tool Website
Annotates and/or filters SNPs, insertions, and deletions for any study design. ANNOVAR [52] http://annovar.openbioinformatics.org/en/latest/
Biofilter [165] https://ritchielab.org/software/biofilter-download-1
Myvariant.info [53] http://myvariant.info
aSnpEff [27] http://snpeff.sourceforge.net
SNPnexus [166] http://www.snp-nexus.org
VCFanno [167] https://github.com/brentp/vcfanno
VEP [35] https://useast.ensembl.org/info/docs/tools/vep/index.html
Annotates GWAS SNPs based on functional information and visualizes results FUMA [137] http://fuma.ctglab.nl
INFERNO [136] http://inferno.lisanwanglab.org/index.php
Associate SNP with phenotype information mediated by gene expression data. COLOC http://cran.r- project.org/web/packages/coloc
eCAVIAR [168] http://genetics.cs.ucla.edu/caviar/index.html
enoloc [122] https://github.com/xqwen/integrative
FOCUS [134] https://github.com/bogdanlab/focus
PrediXcan [128] https://github.com/hakyimlab/PrediXcan
SMR [169] https://cnsgenomics.com/software/smr/#Overview
TWAS [125] http://gusevlab.org/projects/fusion/
UTMOST [132] https://github.com/Joker-Jerome/UTMOST/
Methods that generated predictive scores that suggest a SNP may influence a molecular phenotype. CADD [40] https://cadd.gs.washington.edu
DANN [170] https://cbcl.ics.uci.edu/public_data/DANN/
FIRE [171] https://sites.google.com/site/fireregulatoryvariation/
LINSIGHT [142] https://github.com/CshlSiepelLab/LINSIGHTCA
  1. aSNPeff also has the ability to perform visualization