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

Input

Name (Type)
Description
Pattern

wigs (file)

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.

*.{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}

centromere (file)

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

*.{txt}

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

rds (file)

R data file (.rds) containing panel of normals data, medians of each bin.

*.rds

txt (file)

Text file containing panel of normals data, medians of each bin.

*.txt
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