check SNPs coding or not ?

locate_coding_snps.sh

+SINGULARITY_SIMG=snpsdata_analysis.simg
+singularity shell $SINGULARITY_SIMG
+## select SNPs on an exon|CDS|mRNA|gene
+
+intersect_vcf_annotation () {
+    #1 output prefix
+    #2 vcf
+    #3 gff3
+    #4 exon|CDS|mRNA|gene
+
+  bedtools intersect -wb -a $2 -b $3 | grep $4 | rev | cut -f10- | rev | uniq > $1_$4.bed
+  wait;
+  cat <(head $2) $1_$4.bed > $1_$4.vcf
+}
+
+# diplodus sargus
+for annot in `echo "exon CDS mRNA gene"`; do intersect_vcf_annotation "diplodus" "raw/dip_adaptive_413.vcf" "annotation/sar_annotation.gff3" ${annot} ; done
+# mullus surmuletus
+for annot in `echo "exon CDS mRNA gene"`; do intersect_vcf_annotation "mullus" "raw/mul_adaptive_291.vcf" "annotation/mullus_annotation.gff3" ${annot} ; done