CRC_article

Collection of scripts for analyzing DBS data from colorectal cancer samples

Introduction

Paired tumor/normal whole-genome samples were sequenced with linked-read sequencing technology (DBS technology).

In this repo we will summarize the analysis steps with the main scripts, versions and parameters applied in every section.

Main steps of the analysis

Reference genome (GRCh38): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

1. BLR analysis
2. Copy number analysis
   • TitanCNA (linked-reads workflow)
   • ASCAT (maftools workflow)
   • Cnvkit
3. Structural variant analysis
   • NAIBR
   • LinkedSV
4. Small (somatic) mutation analysis
   • Lancet
   • Maftools
5. RNAseq analysis
   • R scripts