modules/ascat
copy number profiles of tumour cells.
Input
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)
]
} 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} allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
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
GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content
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).