Description

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

Input

Name
Description
Pattern

0 ()

1 ()

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3 ()

4 ()

5 ()

6 ()

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

gccontent_profile (file)

File with GC-content profile

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

controlfreec/freec Documentation

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

https://github.com/BoevaLab/FREEC/doi: 10.1093/bioinformatics/btq635License: GPL >=2
Authors