SVS 7.6.7 features new tools for filtering sequencing data based on functional predictions and allele frequencies. To complement these new features, new annotations tracks have been uploaded to our data server and are now available for our customers! Below you will find descriptions of the new tools and the related annotations track(s).

Filter on Variant Frequency Catalog

This new feature simplifies the process of filtering down to rare variants. What used to take several steps can now be accomplished with one tool! This feature is available in the Select > Filter by Annotation menu and must be used in conjunction with an annotation track that contains an allele frequency field. There are two new annotation tracks that serve this purpose as well.

1kG Phase1 – Variant Frequencies 2012_04_26 v3, GHI contains the latest variant frequencies from 1000 Genomes. The track contains minor allele frequency fields for each subpopulation: Europeans, Asians, Africans and Admixed Americans, as well as a MAF field over all samples.

NHLBI ESP6500 Exomes – Variant Frequencies 2012_06, GHI contains the latest frequencies from the NHLBI Exome Sequencing Project. The track contains allele frequency fields for each subpopulation: European Americans and African Americans, as well as a MAF field over all samples.

To filter based on a particular subpopulation, choose the appropriate field in the filtering dialog. These tracks are only available for the human build GRCH_37.

Filter on Non Synonymous Functional Predictions

This new feature allows the user to filter out variants that are predicted as tolerated or benign based on the following functional predictions: SIFT, PolyPhen, MutationTaster, GERP++, PhyloP. The user may choose to apply only one functional prediction filter or several simultaneously. This filtering tool is also available in the Select > Filter by Annotation menu and must be used with the dbNSFP NS Functional Predictions Track, available for human builds NCBI_36 and GRCH_37. If the track(s) have not yet been downloaded, an auto-detect/auto-download feature in the filtering tool will download it for you.