name: ichorcna_createpon description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals keywords: - ichorcna - cnv - cna - cfDNA - wgs - panel_of_normals tools: - ichorcna: description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. homepage: https://github.com/broadinstitute/ichorCNA documentation: https://github.com/broadinstitute/ichorCNA/wiki tool_dev_url: https://github.com/broadinstitute/ichorCNA doi: "10.1038/s41467-017-00965-y" licence: ['GPL v3'] input: - wigs: type: file description: Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals. pattern: "*.{wig}" - gc_wig: type: file description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window pattern: "*.{wig}" - map_wig: type: file description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window pattern: "*.{wig}" - centromere: type: file description: Text file giving centromere locations of each genome, to exclude these windows pattern: "*.{txt}" output: - versions: type: file description: File containing software versions pattern: "versions.yml" - rds: type: file description: R data file (.rds) containing panel of normals data, medians of each bin. pattern: "*.rds" - txt: type: file description: Text file containing panel of normals data, medians of each bin. pattern: "*.txt" authors: - "@sppearce"