demo-cloningE.sh

Demo for WGS data from a cancer patient

: ex: set ft=markdown ;:<<'```shell' #

The following CHISEL demo represents a guided example of the CHISEL pipeline starting from the inferred copy numbers (typically the file calls.tsv in the folder calls) for tumor section E of breast cancer patient S0, and thus identifies the clones and produces the corresponding plots. Simply run this file through BASH as a standard script to run the complete demo. The demo represent a guided example for the command chisel-cloning which allows to re-run the inference of clones and can be used to try different parameters to explore different solutions and clustering of cells..

Requirements and set up

The demo requires that CHISEL has been succesfully installed with conda. The demo includes the downloading of all the required files and will terminate in <20 minutes on machine with minimum requirements satisfied.

We gurantee that the running directory in the same directory of the demo and we remove previous results.

cd $( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )
rm -rf rdr/ baf/ combo/ calls/ clones/ plots/
:<<'```shell' # Ignore this line

We also ask the demo to terminate in case of errors and to print a trace of the execution by the following commands

set -e
set -o xtrace
PS4='[\t]'
:<<'```shell' # Ignore this line

Downloading of data

The demo auomatically downloads the required inferred copy numbers already computed by the complete CHISEL pipeline in data folder.

# Creating data folder
mkdir -p data

# Downloading copy numbers inferred by CHISEL for tumor section E
curl -L https://github.com/raphael-group/chisel-data/raw/master/demos/cloningE/calls.tsv.gz > data/calls.tsv.gz
gzip -df data/calls.tsv.gz
export INPUT="data/calls.tsv"
:<<'```shell' # Ignore this line

Run CHISEL

We now run the command CHISEL command that starts from the inference of copy numbers from RDRs and BAFs.

chisel_cloning ${INPUT} --seed 25
exit $?