This repository contains a reimplementation of the ASCAT algorithm designed to work with segments computed by GATK's ModelSegments tool. In addition, the implementation can use TP53 VAFs as additional evidence in the model selection process. Overall, the model selection process is slightly different from the original ASCAT algorithm, as it uses a penalized score instead of step-by-step relaxation of constraints until a model is found.
Usage: ./ascat-on-gatk.R [options] segment_model_file
Options:
--snp-purity=SNP-PURITY
Optional truncal SNP (TP53, for example) for for additional purity evidence. Format: chrom,pos,altCount,refCount
--sample=SAMPLE
The sample identifier
--segment-output=SEGMENT-OUTPUT
Output tsv file for the segments
--estimate-output=ESTIMATE-OUTPUT
Output tsv file for purity, ploidy, and goodness of fit
--sunrise-output=SUNRISE-OUTPUT
Output file for the sunrise plot
-h, --help
Show this help message and exit
Written by Kari Lavikka
Licenced under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.