modules/ichorcna_run
ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA
Description
ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA
Input
hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window
*.{wig}
hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window
*.{wig}
hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window
*.{wig}
hmmcopy/readCounter processed .wig file giving the number of reads in the normal sample, in each genomic window
*.{wig}
Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc.
*.{rds}
Text file giving centromere locations of each genome, to exclude these windows
*.{txt}