AgileVariantViewer

Description

AgileVariantViewer allows sequence variants (identified by AgileAnnotator and optionally filtered by AgileKnownSNPFilter) to be interactively displayed and filtered. The variant filtering is adjustable using cut-off parameters for read depth and minor allele frequency. Variants can also be selected according to their position in a gene (exon, intron, splice site or Kozak start site). It is also possible to select variants based on their type (SNP or indel) or the predicted severity of effect on protein function.

If the sequence variants have been filtered by AgileKnownSNPFilter, it is also possible to display SNPs according to whether they have an RS number, have been identified by the 1000 Genomes Project or have not been previously described. By adjusting the read depth and the minor allele frequency parameters, and observing the effect of this on known sequence variants with RS numbers, it is possible to empirically adjust these cut-off values to optimize the detection of true variants.

Once the desired cut-off values have been selected, the sequence variants may be exported from a specified region, from a single chromosome or from the entire genome. It is also possible to export only homozygous variants or heterozygous variants.

Guide to use of AgileVariantViewer

The AgileVariantViewer user guide can be found here.

A short walk-through example guide, in which an analysis is performed of a dataset to identify a disease variant in the ATOH7 gene, can be found here.

Download

The AgileVariantViewer program can be downloaded from my departments wed site here