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