Description

copy number profiles of tumour cells.

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 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 https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/.

*.{bam,cram}

index_normal (file)

index for normal_bam/cram

*.{bai,crai}

input_tumor (file)

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

*.{bam,cram}

index_tumor (file)

index for tumor_bam/cram

*.{bai,crai}

allele_files (file)

allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS

loci_files (file)

loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS 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)

Output

Name (Type)
Description
Pattern

meta (map)

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

]

allelefreqs (file)

Files containing allee frequencies per chromosome

*{alleleFrequencies_chr*.txt}

metrics (file)

File containing quality metrics

*.{metrics.txt}

png (file)

ASCAT plots

*.{png}

purityploidy (file)

File with purity and ploidy data

*.{purityploidy.txt}

segments (file)

File with segments data

*.{segments.txt}

versions (file)

File containing software versions

versions.yml
included in
sarek
authors
Github user aasNGC Github user lassefolkersen Github user FriederikeHanssen Github user maxulysse Github user SusiJo
get in touch
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Tools

ascat
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).

github.com/VanLoo-lab/ascat[...]man https://github.com/VanLoo-lab/ascat 10.1093/bioinformatics/btaa538