How JGA dataset was generated (GRCh38)
JGA-NGS
We performed variant calling of individual-level genomic data deposited at JGA by using the reference sequence GRCh37. Analysis pipeline software (Amelieff BioReT Ver.3.3.1.1) that can execute the following group of analysis tools was used. Additionally, we used transanno to convert GRCh37-based variant data to GRCh38-based one.
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 |