Create 04_run_calls.fix.sh

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