Features

Features

The Bamformatics toolkit has a number of unique and distinguishing features.

Unified options

An important feature is the unification of many options related to data post-processing. For example, it is well known that first/last bases in HTS reads are less reliable than bases located in the middle. The Bamformatics toolkit makes it possible to deal with this issue consistently through many analysis steps that may include variant calling, variant post-processing, error estimation, and computation of various genomic tracks.

Efficiency

Another important feature is computational efficiency. The Bamformatics variant caller is designed for use with medium- to high-coverage samples, which are becoming the norm in exome-seq and RNA-seq applications. On such samples, the caller can process a 5GB alignment in less than 15 minutes producing comparable results to other slower programs designed for low-coverage applications.

It also assumes that processing will be carried out on machines with generous amounts of memory. The minimum recommended RAM is 8GB.

GUI

Bamformatics can be run in graphical mode ([GUI]). This is helpful to users wanting to experiment with the available variant-calling and variant filtering options and to enable fast changes between distinct configurations. The GUI also helps in viewing output files.