Abstract:
Next Generation Sequencing (NGS) has made possible the parallel analysis of sequencing data.
Different NGS platforms are generating huge amount of data. This data undergoes different
analysis pipeline depending upon the platform from which it is produced. Bioinformatics has
made this analysis easier by the development of different tools and pipelines. Several pipelines
are available for performing different types of analysis which includes variant calling,
phylogenetic analysis and many others. In variant calling, once the variants have been called, it is
important to identify their biological significance and their location in the genome. This can be
helpful to identify their roles in different disease. Several tools are available for this purpose.
Each tool has its own features, with certain limitations. Some tools require the annotation sets
from the user, while others require programming skills to use it. So, an automated pipeline is
required to overcome these limitations. This thesis provides the detail about an automated
pipeline implemented in R programming language named as AutoAnnotate. AutoAnnotate takes
only the VCF file as an input and generates the annotation results for the user, along with
different charts and tables representing annotation information in different ways.
