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
Description
Pattern

0 ()

1 ()

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}

normal_wig (file)

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

*.{wig}

normal_background (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}

rep_time_wig (file)

Replication/timing .wig file.

*.{wig}

exons (file)

BED file for exon regions to annotate CNA regions.

*.{bed}

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

ichorcna Documentation

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

https://github.com/broadinstitute/ichorCNAdoi: 10.1038/s41467-017-00965-yLicense: GPL v3
Authors