A Snakemake Pipeline for the Study of Genomic Instability

A Snakemake pipeline for the bioinformatics analysis of genomic instability from NGS data with normal/tumor pair.

This Snakemake pipeline take aligned BAM files from germline/diagnosis samples as input and perform:

1. GATK Best Practices Preprocessing

2. Variant Calling using:

   • Mutect2 (GATK4)

   • Strelka2 + Manta

3. Ploidy/Cellularity analysis using:

   • Sequenza

4. (TODO) Add Williams et al, 2018 and/or Mobster package (Caravagna et al, 2019 preprint)