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Overview over nf-core/sarek. The pipeline consists of three sections: pre-processing based on GATK Best-practice recommendations (mapping, duplicate marking, and base quality score recalibration), variant calling supporting tools for SNP/Indel, SV, CNV, MSI calling and annotation. Throughout the pipeline, various quality control tools are run and collated into a comprehensive MultiQC report. The variant calling tools can be mixed in any combination and are all run in parallel.
