Just a simple tool for converting output from the GATK Somatic Copy Number Workflow to something which can be used as input for ASCAT.
Three files produced by GATK are needed as input. These are the allelic counts at heterozygous sites for the tumor and normal samples, respectively, as well as the denoised copy number ratios. In the official GATK workflow, these files are named SAMPLE.hets.tsv, SAMPLE.hets.normal.tsv, and SAMPLE.denoisedCR.tsv.
The gatk2ascat command is then run as follows:
gatk2ascat --denoised-copy-ratios SAMPLE.denoisedCR.tsv
--allelic-counts-tumor SAMPLE.hets.tsv
--allelic-counts-normal SAMPLE.hets.normal.tsv
--ascat-baf-tumor Tumor_BAF.txt
--ascat-baf-normal Germline_BAF.txt
--ascat-logr-tumor Tumor_LogR.txt
--ascat-logr-normal Germline_LogR.txt
and produces four output files (Tumor_BAF.txt, Germline_BAF.txt, Tumor_LogR.txt, and Germline_LogR.txt) ready for use as input for ASCAT.
The simplest way to install gatk2ascat is by using conda:
$ conda install -c micknudsen gatk2ascat