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. Users can flexibly use RefSeq genes, UCSC genes, ENSEMBL genes, GENCODE genes, or many other gene definition systems.
• 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 H3K4Me1/H3K4Me3/H3K27Ac/CTCF 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 functionalities: 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.

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.

In a modern desktop computer (3GHz Intel Xeon CPU, 8Gb memory), for 4.7 million variants, ANNOVAR requires ~4 minutes to perform gene-based functional annotation, or ~15 minutes to perform stepwise "variants reduction" procedure, making it practical to handle hundreds of human genomes in a day.