This repository contains all code used in the analysis of MYC, BCL2, and BCL6 rearrangements from targeted capture, whole genome, and RNAseq data of Burkitt lymphoma (BL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and high-grade B-cell lymphoma, double hit with MYC and BCL2 or BCL6 rearrangements (HGBCL-DH-BCL2/HGBCL-DH-BCL6). All R packages used in the analysis can be installed reproducibly with renv, using R version 4.1.*. Outputs can be regenerated with the included Snakefile:
snakemake -j5 all
Sequencing files were processed outside of this repository using modules from LCR-Modules as follows:
| Sequencing Type | Output | Module(s) |
|---|---|---|
| genome, capture | Somatic variant calls | slms_3-1.0, vcf2maf-1.3 |
| genome, capture | Somatic structural variants | svar_master-1.0 |
| genome, capture | Quality control (coverage metrics) | qc-1.0 |
| RNAseq | Immunoglobulin rearrangements | mixcr-1.2 |
| RNAseq | Expression | salmon-1.1 |