Friday, 20 January 2012

VarSifter: a useful software to manage NGS data

For beginners (like us) in Next Generation Sequencing data analysis, to find a tool that offers a simple and user friendly manner to analyse and visualize the huge ammount of data produced by exome sequencing, it's like to see a oasis in the vastness of a desert. This is the feeling I had when I started to use VarSifter for the first time.

"VarSifter is a program designed to view massively parallel sequencing variation output. It allows sorting on any field (as well as combinations of fields), and filtering on different types of information (variant type, inheritance, etc). Additionally, it allows custom filtering. The program is written in Java, and should run on any platform with a current Java Virtual Machine." This is the description provided by the authors of the program, Dr. Jamie K. Teer and Dr. James C. Mullikin of the National Human Genome Research Institute (NHGRI) at NIH.
The software allows to use several filters that permit to analyse and compare a multiple types of data related to genome variants. A set of precomputed tools allows, for example, to set which are your control and case samples, which are the affected or normal samples. From this point on it is possible to analyze the data by applying many other filters. For example I can filter for those variants presents only in case samples but not in controls, or discriminate the homozygous variants from the heterozygous ones and so on. Furthermore VarSifter offers the possibilty to create a personalized set of filters on the basis of your needs. You can see a presentation of VarSifter made by Dr. Teer here, and find here the paper describing the software on Bioinformatics.
The NGS technologies allow the generation of an incredible amount of data. Softwares like VarSifter can help us to find the path in this infinite land full.

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