Description

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

Input

Name (Type)
Description
Pattern

args (map)

Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
Parameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. sex = meta.sex:
For default values, please check the documentation above.

{  
  [  
    "general" :[  
        "bedgraphoutput": (optional),  
        "breakpointthreshold": (optional),  
        "breakpointtype": (optional),  
        "coefficientofvariation": (optional),  
        "contamination": (optional),  
        "contaminationadjustment": (optional),  
        "degree": (optional),  
        "forcegccontentnormalization": (optional),  
        "gccontentprofile": (optional),  
        "intercept": (optional),  
        "mincnalength": (optional),  
        "minmappabilityperwindow": (optional),  
        "minexpectedgc": (optional),  
        "maxexpectedgc": (optional),  
        "minimalsubclonepresence": (optional),  
        "noisydata": (optional),  
        "ploidy": (optional),  
        "printNA": (optional),  
        "readcountthreshold": (optional),  
        "sex": (optional),  
        "step": (optional),  
        "telocentromeric": (optional),  
        "uniquematch": (optional),  
        "window": (optional)  
    ],  
    "control":[  
        "inputformat": (required),  
        "mateorientation": (optional),  
    ],  
    "sample":[  
        "inputformat": (required),  
        "mateorientation": (optional),  
    ],  
    "BAF":[  
        "minimalcoverageperposition": (optional),  
        "minimalqualityperposition": (optional),  
        "shiftinquality": (optional)  
    ]  
  ]  
}

meta (map)

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

]

mateFile_normal (file)

File with mapped reads

*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}

mateFile_tumor (file)

File with mapped reads

*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}

cpn_normal (file)

Raw copy number profiles (optional)

*.cpn

cpn_tumor (file)

Raw copy number profiles (optional)

*.cpn

minipileup_normal (file)

miniPileup file from previous run (optional)

*.pileup

minipileup_tumor (file)

miniPileup file from previous run (optional)

*.pileup

fasta (file)

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

*.{fasta,fna,fa}

fai (file)

Fasta index

*.fai

snp_position (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 (file)

File with known SNPs

*.{vcf,vcf.gz}

known_snps_tbi (file)

Index of known_snps

*.tbi

chr_directory (file)

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

*/

mappability (file)

Contains information of mappable positions (optional)

*.gem

target_bed (file)

Sorted bed file containing capture regions (optional)

*.bed

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bedgraph (file)

Bedgraph format for the UCSC genome browser

.bedgraph

control_cpn (file)

files with raw copy number profiles

*_control.cpn

sample_cpn (file)

files with raw copy number profiles

*_sample.cpn

gcprofile_cpn (file)

file with GC-content profile.

GC_profile.*.cpn

BAF (file)

file B-allele frequencies for each possibly heterozygous SNP position

*_BAF.txt

CNV (file)

file with coordinates of predicted copy number alterations.

*_CNVs

info (file)

parsable file with information about FREEC run

*_info.txt

ratio (file)

file with ratios and predicted copy number alterations for each window

*_ratio.txt

config (file)

Config file used to run Control-FREEC

config.txt
included in
sarek
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub

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