diff --git a/fst_analysis/04_run_calls.fix.sh b/fst_analysis/04_run_calls.fix.sh new file mode 100644 index 0000000..2eda28e --- /dev/null +++ b/fst_analysis/04_run_calls.fix.sh @@ -0,0 +1,25 @@ +#Script written by Steven Van Belleghem (2024) + +#!/bin/bash -l +#SBATCH --cluster=genius +#SBATCH --job-name bwa +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=10 +#SBATCH --time=20:00:00 +#SBATCH -A lp_svbelleghem + +# This variable will store the job array number minus 1, so we can use it to get a sample from the samples list (index +starts at 0) +ID=$((SLURM_ARRAY_TASK_ID -1)) + +# Load the programs we will use +module load Python/3.7.0-foss-2018a +module load tabix +export PYTHONPATH=$PYTHONPATH:/vsc-hard-mounts/leuven-data/350/vsc35085/programs/genomics_general + +REFNAME=dudPrim +#REFNAME=nieuPrim + +names=(1 10 2 3 4 5 6 7 8 9) + +zcat /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").calls.gz | sed 's/.dudPrim.filtered.sorted.nd.bam//g' | bgzip > /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").H.calls.gz