Calls CNVs in bam files from tumor patients
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
normal{:bash}
:file
BAM files
*.bam
normal_index{:bash}
BAM file indices
*.bam.bai
tumor{:bash}
tumor_index{:bash}
bed{:bash}
annotated BED file containing target regions
*.bed
fasta{:bash}
genome FASTA file
*.fasta
png{:bash}
PNG file containing profile plot
*.profile.png
*.profile.png{:bash}
profile{:bash}
*.profile.txt{:bash}
TXT file containing profile data
*.profile.txt
summary{:bash}
*.summary.txt{:bash}
TXT file containing summarized data
*.summary.txt
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
a package to detect copy number changes in Deep Sequencing data
