TNscope

Sentieon TNscope basic pipeline

Authors: Massimiliano Volpe, Jyotirmoy Das
Email: massimiliano.volpe@liu.se, jyotirmoy.das@liu.se
Date: 28/01/2021

Developed on behalf of the Bioinformatics Core Facility, Linköping University

Rules:

• Raw data from matched tumor/normal samples should be stored in different folders but named the same, e.g.:
  /path_to_normal/256_S1_R1_001.fastq.gz
  /path_to_tumor/256_S1_R1_001.fastq.gz
• Paths to raw data and reference must be set in the config.json file.
• Fastq filename suffix must be set in the config.json file, e.g.:
  /path_to_normal/256_S1_R1_001.fastq.gz --> "_R1_001.fastq.gz"
  /path_to_normal/256_S1_R2_001.fastq.gz --> "_R2_001.fastq.gz"