Create 03_run_calls.sh

fst_analysis/03_run_calls.sh

@@ -0,0 +1,43 @@
+#Script written by Steven Van Belleghem (2024)
+
+#!/bin/bash -l 
+#SBATCH --cluster=genius 
+#SBATCH --job-name calls 
+#SBATCH --nodes=1 
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=20:00:00 
+#SBATCH -A lp_svbelleghem
+
+ID=$((SLURM_ARRAY_TASK_ID -1))
+
+# Load the programs we will use
+module load Python/3.7.0-foss-2018a
+#export PYTHONPATH=$PYTHONPATH:/vsc-hard-mounts/leuven-data/350/vsc35085/programs/genomics_general
+module load tabix
+
+#module load BCFtools
+
+echo "================="
+
+chrom=(CM008230.1_RagTag CM008231.1_RagTag CM008233.1_RagTag CM008234.1_RagTag CM008235.1_RagTag CM008236.1_RagTag CM008237.1_RagTag CM008238.1_RagTag CM008239.1_RagTag CM008240.1_RagTag)
+names=(1 10 2 3 4 5 6 7 8 9)
+#REFNAME=dudPrim
+REFNAME=nieuPrim
+
+#bcftools view /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.fix.vcf.gz --regions $(echo "${chrom[ID]}") | gzip > /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").vcf.gz
+
+vcftools --gzvcf /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").vcf.gz --recode --remove-indels --minQ 30 --max-missing 0.25 --stdout | bgzip > /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").filt.vcf.gz
+
+python /vsc-hard-mounts/leuven-data/350/vsc35085/programs/parseVCF.py \
+--minQual 30 \
+--skipIndels \
+-i /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").filt.vcf.gz  | \
+gzip > /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").calls.gz
+
+
+zcat /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").calls.gz | sed 's/.nieuPrim.filtered.sorted.nd.bam//g' | gzip > /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$(echo "${names[ID]}").H.calls.gz
+
+
+#--gtf flag=GQ min=30 gtTypes=Het \
+#--gtf flag=GQ min=30 gtTypes=HomAlt \
+#--gtf flag=DP min=10 max=100 \