from a table select only nonsynonymous variants

keep_synonymous.sh

+anvage synonymous --vcf diplodus_CDS.vcf \
+--genome genomes/diplodus_genome_lgt6000.fasta \
+--annotation annotation/sar_annotation.gff3 \
+--output_prefix diplodus_CDS
+
+vcftools --positions <(awk '{print $1" "$2}' diplodus_CDS_uniprot_blast_filtered.tsv | sort | uniq) --vcf diplodus_CDS_nonsynonymous.vcf --recode --out diplodus_CDS_uniprot_nonsynonymous
+
+grep -v "^#" diplodus_CDS_uniprot_nonsynonymous.recode.vcf | awk '{ print $1"\t"$2}' | while read CHROMPOS; do grep "$CHROMPOS" diplodus_CDS_uniprot_blastx.tsv; done > diplodus_CDS_uniprot_nonsynonymous.tsv
+
+
+nonsynonymous_chrompos () {
+#1 vcf input
+#2 genome fasta 
+#3 genome gff3
+#4 prefix
+#5 uniprot table
+anvage synonymous --vcf $1 \
+--genome $2 \
+--annotation $3 \
+--output_prefix $4
+
+vcftools --positions <(awk '{print $1" "$2}' $5 | sort | uniq) --vcf $4"_nonsynonymous.vcf" --recode --out $4"_uniprot_nonsynonymous"
+grep -v "^#" $4"_uniprot_nonsynonymous.recode.vcf" | awk '{ print $1"\t"$2}' | while read CHROMPOS; do grep "$CHROMPOS" $5; done > $4"_uniprot_nonsynonymous.tsv"
+
+}
+
+nonsynonymous_chrompos("mullus_CDS.vcf", "genomes/mullus_genome_lgt6000.fasta","annotation/mullus_annotation.gff3", "mullus_CDS","mullus_CDS_uniprot_blast_filtered.tsv")
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