ASCAT Resources

Current software version is 3.0.0.

Source files for Software .

ASCAT requires a set of external reference data that are provided as additional data sources in the main repository of the software, here. For convenience, we collected and packaged these resources into a single tar archive that contains the following set of files.

Loci Files

ASCAT repository commit 7fc8c9d, files version 20092021

Loci files contain SNP positions derived from the 1000Genomes prepared for hg38/GRCh38, available here. We operate on chr-based bam files, so the original loci files were modified and the chr- prefix was added by running the command:

for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg38_chr${i}.txt; done

Allele Files

ASCAT repository commit 7fc8c9d, files version 20092021

Allele files contain SNP positions with their reference and alternative nucleotide bases based on the 1000Genomes prepared for hg38/GRCh38, available here.

GC Correction File

ASCAT repository commit 7fc8c9d, files version 20092021

The GC correction file contains the GC content around every SNP for increasing window sizes, available here.