Description

Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

coverage_files (file)

Coverage files from normal samples

*.txt.gz

normal_vcf (file)

Normal panel in VCF format, used to precompute mapping bias
for faster runtimes. Optional.

*.vcf.gz

genome (string)

Genome build

assay (string)

Assay name

Output

Name (Type)
Description
Pattern

rds (file)

File containing the generated panel of normals

normalDB*.rds

png (file)

Plot of interval weights calculated from the panel of normals

interval_weights*.png

bias_rds (file)

Calculated mapping bias from the normal files

mapping_bias*.rds

bias_bed (file)

Calculated mapping bias sites from the normal files

mapping_bias_hq_sites*.bed

low_cov_bed (file)

BED with possibly low coverage targets identified, only
generated if there are low coverage targets

low_coverage_targets*.bed

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