How JGA dataset was generated
JGA-NGS
Analysis pipeline software (Amelieff BioReT Ver.3.3.1.1) that can execute the following group of analysis tools was used.
| Tool name | Version |
| qcleaner | 4.1.0 |
| SAM tools | 1.6 |
| FastQC | 0.11.5 |
| calcCoverage | 1.7 |
| BWA | 0.7.16a |
| igvtools | 2.3.98 |
| Picard | 2.13.2 |
| GATK | 3.8.0-ge9d806836 |
| SnpEff | v4.3_core |
| bedtools | 2.13.3 |