otari/variant_effect_prediction.sh at main · FunctionLab/otari · GitHub

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#!/bin/bash
#SBATCH -t 0-01:0
#SBATCH -p gpu
#SBATCH --gpus-per-task=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --output=logfiles/slurm-%j.out
#SBATCH --mem=100G

mkdir -p logfiles

vcf_filepath="${1:-}"  # path to vcf file
outdir="${2:-}"        # path to output dir
annotate="${3:-true}"  # whether to annotate
visualize="${4:-false}" # whether to visualize results

if [ "$visualize" = "true" ]; then
    if [ "$annotate" = "true" ]; then
        python variant_effect_prediction.py \
            --variant_path $vcf_filepath \
            --output_path $outdir \
            --annotate \
            --visualize
    else
        python variant_effect_prediction.py \
            --variant_path $vcf_filepath \
            --output_path $outdir \
            --visualize
    fi
else
    if [ "$annotate" = "true" ]; then
        python variant_effect_prediction.py \
            --variant_path $vcf_filepath \
            --output_path $outdir \
            --annotate
    else
        python variant_effect_prediction.py \
            --variant_path $vcf_filepath \
            --output_path $outdir
    fi
fi