ANNOVAR

Description

annovar website

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: Gene-based annotation: identify whether SNPs or CNVs cause protein coding changes and the amino acids that are affected. Region-based annotations: identify variants in specific genomic regions, for example, conserved regions among 44 species, predicted transcription factor binding sites, segmental duplication regions, GWAS hits, database of genomic variants, DNAse I hypersensitivity sites, ENCODE sites, ChIP-Seq peaks, RNA-Seq peaks, or many other annotations on genomic intervals. Filter-based annotation: identify variants that are reported in dbSNP, or identify the subset of common SNPs (MAF>1%) in the 1000 Genome Project, or identify subset of non-synonymous SNPs with SIFT score > 0.05, or many other annotations on specific mutations. Other functionality: Retrieve the nucleotide sequence in any user-specific genomic positions in batch, identify a candidate gene list for Mendelian diseases from exome data, identify a list of SNPs from 1000 Genomes that are in strong LD with a GWAS hit, and many other creative utilities.

Environment Modules

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

Environment Variables

• HPC_ANNOVAR_DIR - installation directory

Additional Usage Information

SUMMARIZE_ANNOVAR is a script within the ANNOVAR package that is very popular among users. Given a list of variants from whole-exome or whole-genome sequencing, it will generate an Excel-compatible file with gene annotation, amino acid change annotation, SIFT scores, PolyPhen scores, LRT scores, MutationTaster scores, PhyloP conservation scores, GERP++ conservation scores, dbSNP identifiers, 1000 Genomes Project allele frequencies, NHLBI-ESP 5400 exome project allele frequencies and other information.

Citation

If you publish research that uses annovar you have to cite it as follows:

Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data, Nucleic Acids Research, 38:e164, 2010

Categories

biology, genomics