You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
58 lines
1.9 KiB
YAML
58 lines
1.9 KiB
YAML
name: ichorcna_createpon
|
|
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
|
|
keywords:
|
|
- ichorcna
|
|
- cnv
|
|
- cna
|
|
- cfDNA
|
|
- wgs
|
|
- panel_of_normals
|
|
tools:
|
|
- ichorcna:
|
|
description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
|
|
homepage: https://github.com/broadinstitute/ichorCNA
|
|
documentation: https://github.com/broadinstitute/ichorCNA/wiki
|
|
tool_dev_url: https://github.com/broadinstitute/ichorCNA
|
|
doi: "10.1038/s41467-017-00965-y"
|
|
licence: ["GPL v3"]
|
|
|
|
input:
|
|
- wigs:
|
|
type: file
|
|
description: 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.
|
|
pattern: "*.{wig}"
|
|
|
|
- gc_wig:
|
|
type: file
|
|
description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window
|
|
pattern: "*.{wig}"
|
|
|
|
- map_wig:
|
|
type: file
|
|
description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window
|
|
pattern: "*.{wig}"
|
|
|
|
- centromere:
|
|
type: file
|
|
description: Text file giving centromere locations of each genome, to exclude these windows
|
|
pattern: "*.{txt}"
|
|
|
|
output:
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
- rds:
|
|
type: file
|
|
description: R data file (.rds) containing panel of normals data, medians of each bin.
|
|
pattern: "*.rds"
|
|
|
|
- txt:
|
|
type: file
|
|
description: Text file containing panel of normals data, medians of each bin.
|
|
pattern: "*.txt"
|
|
|
|
authors:
|
|
- "@sppearce"
|