Description

Run PureCN workflow to normalize, segment and determine purity and ploidy

Input

Name (Type)
Description
Pattern

meta (map)

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

intervals (file)

BED file of target intervals, generated from IntervalFile.R

{*.bed,*.txt}

coverage (file)

Coverage file generated from Coverage.R

*.txt

normaldb (file)

Normal panel in RDS format, generated from NormalDB.R

*.rds

genome (string)

Genome build

Output

Name (Type)
Description
Pattern

pdf (file)

PDF file containing copy number plots

*.pdf

local_optima_pdf (file)

PDF file containing local optima plots

*_local_optima.pdf

seg (file)

Tab-delimited file containing segmentation results

*_dnacopy.seg

genes_csv (file)

CSV file containing gene copy number calls. Optional

*_genes.csv

amplification_pvalues_csv (file)

CSV file containing amplification p-values. Optional

*_amplification_pvalues.csv

vcf_gz (file)

GZipped VCF file containing SNV calls. Optional

*.vcf.gz

variants_csv (file)

CSV file containing SNV calls. Optional

*_variants.csv

loh_csv (file)

CSV file containing LOH calls. Optional

*_loh.csv

chr_pdf (file)

PDF file containing chromosome plots. Optional

*_chromosomes.pdf

segmentation_pdf (file)

PDF file containing segmentation plots. Optional

*_segmentation.pdf

multisample.seg (file)

Tab-delimited file containing segmentation data from multiple samples. Optional

*_multisample.seg

versions (file)

File containing software versions

versions.yml
maintainers
Github user aldosr
Github user lbeltrame
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

purecn
Artistic-2.0

Copy number calling and SNV classification using targeted short read sequencing

args_id: $args
bioconductor.org/packages/release/bioc/html/PureCN https://github.com/lima1/PureCN 10.1186/s13029-016-0060-z