What it does
This tool will annotate a file using ANNOVAR.
ANNOVAR Website and Documentation
Input Formats may be one of the following:
VCF file Complete Genomics varfile
Custom tab-delimited file (specify chromosome, start, end, reference allele, observed allele columns)
Custom tab-delimited CG-derived file (specify chromosome, start, end, reference allele, observed allele, varType columns)
see ANNOVAR website for extensive documentation, a few notes on some of the databases:
PolyPhen2 HVAR should be used for diagnostics of Mendelian diseases, which requires distinguishing mutations with drastic effects from all the remaining human variation, including abundant mildly deleterious alleles.The authors recommend calling probably damaging if the score is between 0.909 and 1, and possibly damaging if the score is between 0.447 and 0.908, and benign if the score is between 0 and 0.446.
PolyPhen HDIV should be used when evaluating rare alleles at loci potentially involved in complex phenotypes, dense mapping of regions identified by genome-wide association studies, and analysis of natural selection from sequence data. The authors recommend calling probably damaging if the score is between 0.957 and 1, and possibly damaging if the score is between 0.453 and 0.956, and benign is the score is between 0 and 0.452.