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