ANNOVAR

ANNOVAR is a software tool that annotates single nucleotide variants (SNVs) and insertions/deletions. This tool is particularly useful in the field of genetics research, where high-throughput sequencing platforms generate massive amounts of genetic variation data. However, it can be a challenge to pinpoint a small subset of functionally essential variants from such large datasets.

The ANNOVAR tool was developed with various features to help researchers annotate and analyze SNVs and insertions/deletions. One of the critical features of ANNOVAR is its ability to examine the functional consequences of SNVs on genes. It can also infer cytogenetic bands, report functional importance scores, identify variants in conserved regions, and find variants reported in the 1000 Genomes Project and dbSNP.

ANNOVAR can utilize annotation databases from the UCSC Genome Browser or any annotation data set conforming to Generic Feature Format version 3 (GFF3). This flexibility allows researchers to easily incorporate external data sources into their analyses.

In addition to its annotation features, ANNOVAR also includes a 'variants reduction' protocol. This protocol is particularly useful for analyzing large datasets of SNVs and insertions/deletions. Through a stepwise procedure, ANNOVAR can exclude unlikely causal variants and identify candidate genes.

ANNOVAR can perform gene-based annotation and variants reduction on millions of variants in a matter of minutes, making it practical to handle hundreds of human genomes daily. This speed and efficiency make ANNOVAR a valuable tool for genetics researchers who need to analyze large datasets quickly.