modules/ascat

index for tumor_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

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

Reference fasta file (optional)

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

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