Esophageal Squamous Dysplasia

Genomic Characterization and Risk Stratification of Esophageal Squamous Dysplasia

Features

Mutational burden
Mutational signature
Driver genes
Genomic landscape
Copy number alterations

Softwares

BWA (v0.7.17)
Picard (v1.119)
GATK4 (v4.1.0.0, MuTect2)
CaVEMan (v1.15.3)
Bcftools (v1.16)
MuSE (v2.0)
cgpPindel (v3.10.0)
Platypus (v0.8.1)
ANNOVAR (v2020Jun7)
CNVkit (v0.9.6)
ABSOLUTE (v1.0.6)
MuSiC2 (v0.2)
COSMIC signatures (v3.3)
SigProfilerExtractor
GISTIC (v2.0.23)

Prerequisites

Linux x86_64 GNU/Linux or UNIX
R >= 3.6.0
perl >= v5.16.3