copy number profiles of tumour cells.


Name (Type)

args (map)

Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.

    "gender": "XX",  
    "genomeVersion": "hg19"  
    "purity": (optional),  
    "ploidy": (optional),  
    "gc_files": (optional),  
    "minCounts": (optional),  
    "BED_file": (optional) but recommended for WES,  
    "chrom_names": (optional),  
    "min_base_qual": (optional),  
    "min_map_qual": (optional),  
    "ref_fasta": (optional),  
    "skip_allele_counting_tumour": (optional),  
    "skip_allele_counting_normal": (optional)  

meta (map)

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


input_normal (file)

BAM/CRAM file, must adhere to chr1, chr2, …chrX notation For modifying chromosome notation in bam files please follow


index_normal (file)

index for normal_bam/cram


input_tumor (file)

BAM/CRAM file, must adhere to chr1, chr2, …chrX notation


index_tumor (file)

index for tumor_bam/cram


allele_files (file)

allele files for ASCAT WGS. Can be downloaded here

loci_files (file)

loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command if [[ $(samtools view <your_bam_file.bam> | head -n1 | cut -f3)\" == \*."chr\"\*.]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi

bed_file (file)

Bed file for ASCAT WES (optional, but recommended for WES)

fasta (file)

Reference fasta file (optional)

gc_file (file)

GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content

rt_file (file)

replication timing correction file (optional, provide only in combination with gc_file)


Name (Type)

meta (map)

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


allelefreqs (file)

Files containing allee frequencies per chromosome


metrics (file)

File containing quality metrics


png (file)

ASCAT plots


purityploidy (file)

File with purity and ploidy data


segments (file)

File with segments data


versions (file)

File containing software versions



GPL v3

ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).