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