Description

Copy number and genotype annotation from whole genome and whole exome sequencing data

Input

name:type
description
pattern

meta{:bash}

:map

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

mpileup_normal{:bash}

:file

miniPileup file

mpileup_tumor{:bash}

:file

miniPileup file

cpn_normal{:bash}

:file

Raw copy number profiles (optional)

*.cpn

cpn_tumor{:bash}

:file

Raw copy number profiles (optional)

*.cpn

minipileup_normal{:bash}

:file

miniPileup file from previous run (optional)

*.pileup

minipileup_tumor{:bash}

:file

miniPileup file from previous run (optional)

*.pileup

fasta{:bash}

:file

Reference file (optional; required if args ‘makePileup’ is set)

*.{fasta,fna,fa}

fai{:bash}

:file

Fasta index

*.fai

snp_position{:bash}

:file

Path to a BED or VCF file with SNP positions to create a mini pileup file from the initial BAM file provided in mateFile (optional)

*.{bed,vcf}

known_snps{:bash}

:file

File with known SNPs

*.{vcf,vcf.gz}

known_snps_tbi{:bash}

:file

Index of known_snps

*.tbi

chr_directory{:bash}

:file

Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)

*/

mappability{:bash}

:file

Contains information of mappable positions (optional)

*.gem

target_bed{:bash}

:file

Sorted bed file containing capture regions (optional)

*.bed

gccontent_profile{:bash}

:file

File with GC-content profile

Output

name:type
description
pattern

bedgraph{:bash}

meta{:bash}

:map

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

*_ratio.BedGraph{:bash}

:file

Bedgraph format for the UCSC genome browser

.bedgraph

control_cpn{:bash}

meta{:bash}

:map

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

*_control.cpn{:bash}

:file

files with raw copy number profiles

*_control.cpn

sample_cpn{:bash}

meta{:bash}

:map

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

*_sample.cpn{:bash}

:file

files with raw copy number profiles

*_sample.cpn

gcprofile_cpn{:bash}

meta{:bash}

:map

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

GC_profile.*.cpn{:bash}

:file

file with GC-content profile.

GC_profile.*.cpn

BAF{:bash}

meta{:bash}

:map

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

*_BAF.txt{:bash}

:file

file B-allele frequencies for each possibly heterozygous SNP position

*_BAF.txt

CNV{:bash}

meta{:bash}

:map

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

*_CNVs{:bash}

:file

file with coordinates of predicted copy number alterations.

*_CNVs

info{:bash}

meta{:bash}

:map

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

*_info.txt{:bash}

:file

parsable file with information about FREEC run

*_info.txt

ratio{:bash}

meta{:bash}

:map

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

*_ratio.txt{:bash}

:file

file with ratios and predicted copy number alterations for each window

*_ratio.txt

config{:bash}

meta{:bash}

:map

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

config.txt{:bash}

:file

Config file used to run Control-FREEC

config.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

controlfreec/freec
GPL >=2

Copy number and genotype annotation from whole genome and whole exome sequencing data.

http://boevalab.inf.ethz.ch/FREEC http://boevalab.inf.ethz.ch/FREEC/tutorial https://github.com/BoevaLab/FREEC/ 10.1093/bioinformatics/btq635
included in
sarek
maintainer
Github user FriederikeHanssen
get in touch
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