feat: feature-complete end-to-end run of the Becnel dataset on hs37d5 & GRCh38.d1.vd1 #460
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…a variant in the translation initiation codon
…rather than a wrapper
…ation in the filtration step
The somatic_cnv_checking step now only accepts DNAcopy format for CNV description. The format is only defined in the DNAcopy reference manual (https://bioconductor.org/packages/release/bioc/manuals/DNAcopy/man/DNAcopy.pdf) BREAKING CHANGE: All tools in the somatic_targeted_cnv_calling step must be changed. (see further commits)
…utation & plots), and replacement of BED to DNAcopy CNV format Behaviour changes to purecn pertaining to CNV description format also rolled in. Those changes are in the workflow file and its tests.
…ry_name), and fix for PureCN bug
…e library_name for coverage compatibility
mbenary
approved these changes
Oct 30, 2023
This was referenced Dec 9, 2024
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This is feature-complete somatic snappy branch, ready for tagging.
sequenza&PureCNCNV calling, required for purity & ploidy, and for homologous recombination deficiency.