Wednesday, August 18, 2010


ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data

ANNOVA is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. Given a list of variants with chromosome, start position, end position and observed nucleotides, ANNOVAR can identify whether SNPs or indels cause protein coding changes and what is the amino acids that were changed, or identify variants in conserved genomic regions, or 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...

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.

REF: Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data Nucleic Acids Research, doi:10.1093/nar/gkq603, 2010

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