GRIDSS/PURPLE/LINX Workflow, used for somatic genomic rearrangement detection and classification on WGS data. This workflow takes a pair of matched tumor/normal BAM files and produces allele-specific copy number of every base of the genome, overall sample purity and ploidy, annotated SV clusters and gene fusion predictions. Moreover, it outputs detailed visualisations of the rearrangements in the tumor genome via integrated Circos plots showing copy number changes, clustered SVs, derivative chromosome predictions and impacted genes.
PURPLE CNV Calling Workflow, used for somatic CNV calling and purity and ploidy estimation on WGS data. It is based on PURPLE 2.51, and consists of two additional tools – AMBER and COBALT. The workflow first calculates B-allele frequency (BAF) with AMBER and read depth ratios with COBALT, which is then used by PURPLE to estimate the purity, ploidy and copy number profile of a tumor sample.