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

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

wig (file)

hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window

*.{wig}

gc_wig (file)

hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window

*.{wig}

map_wig (file)

hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window

*.{wig}

panel_of_normals (file)

Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc.

*.{rds}

centromere (file)

Text file giving centromere locations of each genome, to exclude these windows

*.{txt}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

versions (file)

File containing software versions

versions.yml

cna_seg (file)

Predicted copy number variation per segment

*.{cng.seg}

ichorcna_params (file)

A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc

*.{params.txt}

genome_plot (file)

A plot with the best-fit genome-wide CNV data

*.{genomeWide.pdf}
maintainer
Github user sppearce
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

ichorcna
GPL v3

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

github.com/broadinstitute/ichorCNA github.com/broadinstitute/ichorCNA/wiki https://github.com/broadinstitute/ichorCNA 10.1038/s41467-017-00965-y