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{:bash}

:map

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

wig{:bash}

:file

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

*.{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}

normal_wig{:bash}

:file

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

*.{wig}

normal_background{:bash}

:file

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

*.{rds}

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

rdata{:bash}

meta{:bash}

:map

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

${prefix}.RData{:bash}

:file

RData file containing all the intermediate R objects

*.{cng.seg}

seg{:bash}

meta{:bash}

:map

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

${prefix}.seg{:bash}

:file

Predicted copy number variation per segment

*.{seg}

cna_seg{:bash}

meta{:bash}

:map

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

${prefix}.cna.seg{:bash}

:file

Predicted copy number variation per segment

*.{cng.seg}

seg_txt{:bash}

meta{:bash}

:map

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

${prefix}.seg.txt{:bash}

:file

Predicted copy number variation per segment

*.{seg.txt}

corrected_depth{:bash}

meta{:bash}

:map

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

${prefix}.correctedDepth.txt{:bash}

:file

A text file with corrected depth per bin

*.{params.txt}

ichorcna_params{:bash}

meta{:bash}

:map

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

${prefix}.params.txt{:bash}

:file

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

*.{params.txt}

plots{:bash}

meta{:bash}

:map

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

${prefix}/*.pdf{:bash}

:file

Plots with e.g. individual chromosomes and different considered ploidy

*.{pdf}

genome_plot{:bash}

meta{:bash}

:map

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

**/${prefix}_genomeWide.pdf{:bash}

:file

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

*.{genomeWide.pdf}

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
maintainers
Github user sppearce
Github user adamrtalbot
get in touch
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