SHARC

Jose Espejo Valle-Inclan & Roel Janssen
SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies. We provide packages to run on: SLURM cluster SGE cluster Local Singularity image Docker image https://github.com/UMCUGenetics/SHARC
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