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demo-complete.sh

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Complete demo of CHISEL

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

The following CHISEL demo represents a guided example of the complete CHISEL pipeline starting from an exemplary barcoded BAM file publicly available. From this directory, simply run this file through BASH as a standard script to run the complete demo. The demo can also be considered as a guided example of a complete execution and is correspondingly commented.

Requirements and set up

The demo requires that CHISEL has been succesfully installed with conda. If the custom installation was used, please make sure that you can succesfully run the command chisel as well as the required samtools, bcftools, and awk. 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 barcoded single-cell and matched-normal BAM files in data folder.

# Creating data folder
mkdir -p data

# Downloading tumor barcoded BAM file
echo "Downloading tumor barcoded BAM file from Zenodo, please be patient as downloading time may vary."
curl -L 'https://zenodo.org/record/3950299/files/cells.bam?download=1' > data/cells.bam
curl -L 'https://zenodo.org/record/3950299/files/cells.bam.bai?download=1' > data/cells.bam.bai
export TUM="data/cells.bam"

# Downloading matched-normal BAM file
echo "Downloading matched-normal BAM file from Zenodo, please be patient as downloading time may vary."
curl -L 'https://zenodo.org/record/3950299/files/normal.bam?download=1' > data/normal.bam
curl -L 'https://zenodo.org/record/3950299/files/normal.bam.bai?download=1' > data/normal.bam.bai
export NOR="data/normal.bam"
:<<'```shell' # Ignore this line

Next the corresponding reference genome is downloaded and unpacked

echo "Downloading human reference genome, please be patient as downloading time may vary."
curl -L https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz | gzip -d > data/hg19.fa
samtools faidx data/hg19.fa
samtools dict data/hg19.fa > data/hg19.dict
export REF="data/hg19.fa"
export DIC="data/hg19.dict"
:<<'```shell' # Ignore this line

Last, we download the pre-computed list of phased germline SNPs. Note that differently from the one obtained through the reccommended instructions (i.e. using BCFtools to call germline SNPs and Eagle2 throught the Michigan Imputation Serverve with HRC panel to phase the SNPs) this file only contains the lables 0|1 or 1|0 for every SNP, which is the minimum requirement for CHISEL.

curl -L 'https://zenodo.org/record/3950299/files/phases.tsv?download=1' > data/phases.tsv
export PHA="data/phases.tsv"
:<<'```shell' # Ignore this line

Run CHISEL

We now run the complete pipeline of CHISEL with the corresponding command chisel.

chisel -t ${TUM} -n ${NOR} -r ${REF} -l ${PHA} --seed 12
exit $?