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{:bash}

: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{:bash}

:file

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

*.{wig}

map_wig{:bash}

:file

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

*.{wig}

centromere{:bash}

:file

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

*.{txt}

rep_time_wig{:bash}

:file

Replication/timing .wig file.

*.{wig}

exons{:bash}

:file

BED file for exon regions to annotate CNA regions.

*.{bed}

Output

name:type
description
pattern

rds{:bash}

${prefix}*.rds{:bash}

:file

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

*.rds

txt{:bash}

${prefix}*.txt{:bash}

:file

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

*.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainer
Github user sppearce
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