Description

copy number profiles of tumour cells.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

4 ()

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
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

ascat Documentation

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).

https://github.com/VanLoo-lab/ascatdoi: 10.1093/bioinformatics/btaa538License: GPL v3
Authors