VIVIDHA: Variant Analysis & Visualization Interface for Dynamic High- Throughput Application
VIVIDHA is a tool used for high variant analysis of genomics data using big data technologies.
Brief Description
- With the increasing size of datasets, there is a dire need to develop scalable and cost-effective methodologies for variant calling
- VIVIDHA is based on distribution of mapped files (BAM/SAM) into several overlapping chunks to enable fast computation without compromising on the quality of the called variants
- Several callers have been employed on the sample dataset and a consensus strategy is used to arrive at the 'optimal set of variants'
- VIVIDHA enables variant discovery in low-coverage data and reduce the overall 'False Discovery Rate'
- VIVIDHA has been developed using map-reduce on Hadoop where in data is stored in a distributed manner using HDFS
Platform Required
Apache Hadoop platform
Contact Details
HPC-MBA (High Performance Computing – Medical and Bioinformatics Applications) Group
Email: rajendra[at]cdac[dot]in
Address: HPC-M&BA Group
C-DAC Innovation Park,
Panchavati, Pashan,
Pune - 411 008, Maharashtra (India)
Phone: +91-20-25503100