Important links:

• Tracker issue in genetics/projects repo: https://gitlab.labmed.uw.edu/genetics/projects/issues/100
• Current research pipeline: https://bitbucket.org/nithishak/loh-pipeline/src/master/

This file is dependent on genome build (e.g.: hg19 vs hg38) - go to the genome browser: https://genome.ucsc.edu/cgi-bin/hgTables - select relevant genome build from "assembly" dropdown - select all tables from "group" dropdown - select gap from "table" dropdown - select genome from "region" bullets - click get output This file gives the coordinates of genomic features (including centromere). The LOH scoring script parses this file to decide which segments are in the P vs Q chromosome arms.

Install the nextflow binary in this directory

wget -qO- https://get.nextflow.io | bash

Execute locally, using docker images (must be available via docker locally)

./nextflow run main.nf --tumor tumor_dir/ --normal normal_dir/ --gc hg19.wig --cen hg19.centromere.txt -profile docker