GAMUT - Platform for addressing high throughput analysis and management of variant data produced by Next Generation Sequencing techniques.
Developed by : High Performance Computing - Medical & Bioinformatics Applications Group (HPC-M&BA) at Center for Development of Advanced Computing (C-DAC), Pune, India.
For more details click here
- Accelerated Search : Speed and Optimization are key attributes for any search, Gamut enables these features for search across large genomic databases.
- Graphical Output : Graphical output displays the results in different graphical formats like bar and pie charts.
- Big data Solution : MongoDB is used at backend for support as a big data database solution for life sciences data.
- Variant Comparison : Efficient analysis of Single Nucleotide Polymorphisms (SNPs) across genomic samples enable in deciphering the relationship between genotype and phenotype. The core principle behind SNP comparison is to arrive at a probable list of variants that can differentiate two sets of data (populations). Such SNPs have direct applications in array design, genotype imputation and in cataloging of variants in regions of interest.
- 1000 Genome data : The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project.1000 genomes have provided ~85 million genetic variants (SNPs) that have frequencies of at least 1% in the populations studied (1000 Genomes Project Consortium et al. 2015). The data provides a glimpse of underlying similarities and variations which can be used for genetic differentiation (Enard et al. 2014).
https://github.com/bioinformatics-cdac/gamut
Sample Input data is provided with Gamut installer.
Eight individuals from 1000 Genome Data belonging to different populations have been used as sample data.
A sample VCF file has been generated for the 8 individuals using the following genomic coordinates
| Chromosome | Start | End |
|---|---|---|
| 1 | 10505 | 999999 |
| 2 | 10180 | 999817 |
| 3 | 60069 | 999979 |
| 4 | 10202 | 999992 |
| 5 | 10043 | 999969 |
| 6 | 63854 | 999962 |
| 7 | 14808 | 999995 |
| 8 | 11740 | 1000000 |
| 9 | 10327 | 999972 |
| 10 | 60494 | 999977 |
| 11 | 73015 | 999999 |
| 12 | 60181 | 999935 |
| 16 | 60086 | 999963 |
| 17 | 52 | 999996 |
| 18 | 10644 | 999993 |
| 19 | 60842 | 999975 |
| 20 | 60343 | 1000010 |
| 21 | 9411239 | 9999932 |
| X | 60026 | 999973 |
