ampliconsuitebrainmets

The original code and instructions are from https://github.com/AmpliconSuite/AmpliconSuite-pipeline . It has been modified to generate the seed intervals from the FACETS calls, which are then passed to Amplicon Architect.

Installation

1. Obtain the data repository containing the AmpliconSuite-pipeline image and GRCh37 annotations :

   • Download the data repo: https://datasets.genepattern.org/?prefix=data/modulesupportfiles/AmpliconArchitect
   • Extract the tar file bash tar zxf GRCh38.tar.gz.gz
   • Download the singularity image bash singularity pull library://jluebeck/ampliconsuite-pipeline/ampliconsuite-pipeline
   • Put both inside a folder named data_repo

2. Obtain the execution script bash git clone https://github.com/uretaj/as_brainmets_v2/.git

3. License for Mosek optimization tool:

   • Obtain license file mosek.lic (https://www.mosek.com/products/academic-licenses/). The license is free for academic use.
   • Place the file in $HOME/mosek/ (i.e, the mosek/ folder that now exists in your home directory).

   • If you are not able to place the license in the default location, you can set a custom location by exporting the bash variable MOSEKLM_LICENSE_FILE=/custom/path/.

     bash export MOSEKLM_LICENSE_FILE="/path/to/mosek.lic" An example command might look like:

as_brainmets_v2/singularity/run_paa_singularity.py -o path/to/output_dir/sample --bam sample.bam --scna_file sample.txt --data_repo path/to/data_repo

Below is a sample Slurm file: ```bash

!/bin/bash

SBATCH --job-name=circdna.slurm

SBATCH --ntasks=1

SBATCH -t 48:00:00

SBATCH --cpus-per-task=1

SBATCH --mail-type=ALL

SBATCH --output=%x.%a.%j.out # STDOUT

SBATCH --error=%x.%a.%j.err # STDERR

SBATCH --array=1-40

SBATCH --mem-per-cpu=100G

module load singularity/3.8.2 export MOSEKLMLICENSEFILE="mosek/mosek.lic" echo "ARRAY ID: ${SLURMARRAYTASKID}" filename=$(head -n ${SLURMARRAYTASKID} hlfalistallcountries.csv | tail -1) filename=${filename%$'\r'} IFS=',' read -ra arr <<< "$filename" sample=${arr[0]} cnv=${arr[1]} echo "SAMPLE ${sample}" echo "FILENAME ${cnv}" pathf="BAM/${sample}.mapped.bam" cnvpath="SubclonalSCNAwithAvgCN/${cnv} asbrainmetsv2/singularity/runpaasingularity.py -o AARESULT/${sample} -t 1 --bam ${pathf} --scnafile ${cnvpath} --datarepo path/data_repo ``` Here's an example of how to submit a job arrray to run multiple samples (i.e. execute the script for 40 samples but only run 5 samples at a time)

bash sbatch --array=1-40%5 amplicon_suite.slurm

Command line arguments to AmpliconSuite-pipeline

Required

• -o {outdir}: Directory where results will be stored. Include the sample name to avoid conflicts.
• --data_repo {repodir}: Directory where the singularity image file and required annotations for GRCh38 are stored.
• -t : Number of threads but it's not really used so just set it to 1.

Input files:

• --bam {sample.bam} Coordinate-sorted bam
• --scna_file {scna.txt} Supply the FACETS calls of the sample to generate the seed intervals to be passed to Amplicon Architect.