tuner / ASCAT-for-GATK

Reimplemented ASCAT algorihm for GATK copy-number segments

ASCAT algorithm for GATK segments

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

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

License

Written by Kari Lavikka

Licenced under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.