This repository includes codes for the meta-analysis of acral and mucosal melanomas.
The Pipeline_Scripts folder contains scripts used for:
- Calling somatic mutations (Mutect2 and Strelka2), annotating (ANNOVAR) and filtering
- Calling germline mutations (HaplotypeCaller), annotating (ANNOVAR) and filtering
- Copy number analysis (FACETS, CNVkit and GISTIC2)
- Calling structural alterations (Delly)
- Estimating degree of microsatellite instability (MISsensor)
- Survival analysis (R package survival )
The Figure_Scripts folder includes R scripts used to plot figures in the manuscript.
The Related_Files folder includes some annotation files required by the pipeline.