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{:bash}

:map

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

coverage_files{:bash}

:file

Coverage files from normal samples

*.txt.gz

normal_vcf{:bash}

:file

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

*.vcf.gz

normal_vcf_tbi{:bash}

:file

Normal panel in VCF format

*.vcf.gz.tbi

genome{:bash}

:string

Genome build

assay{:bash}

:string

Assay name

Output

name:type
description
pattern

rds{:bash}

meta{:bash}

:file

File containing the generated panel of normals

normalDB*.rds

normalDB*.rds{:bash}

:file

File containing the generated panel of normals

normalDB*.rds

png{:bash}

meta{:bash}

:file

File containing the generated panel of normals

normalDB*.rds

interval_weights*.png{:bash}

:file

Plot of interval weights calculated from the panel of normals

interval_weights*.png

bias_rds{:bash}

meta{:bash}

:file

File containing the generated panel of normals

normalDB*.rds

mapping_bias*.rds{:bash}

:file

Calculated mapping bias from the normal files

mapping_bias*.rds

bias_bed{:bash}

meta{:bash}

:file

File containing the generated panel of normals

normalDB*.rds

mapping_bias_hq_sites*.bed{:bash}

:file

Calculated mapping bias sites from the normal files

mapping_bias_hq_sites*.bed

low_cov_bed{:bash}

meta{:bash}

:file

File containing the generated panel of normals

normalDB*.rds

low_coverage_targets*.bed{:bash}

:file

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

low_coverage_targets*.bed

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainers
Github user aldosr
Github user lbeltrame
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