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TNscope

Sentieon TNscope basic pipeline

Authors: Massimiliano Volpe, Jyotirmoy Das
Email: [email protected], [email protected]
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"

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