new file: cre.annotate_str.sh

	new file:   cre.annotate_str.toml
	new file:   protein_coding_genes.bed.gz
	new file:   protein_coding_genes.bed.gz.tbi

cre.annotate_str.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+#use cre.annotate_str.sh vcf_from_lobstr.vcf
+
+bname=`echo $1 | sed s/.vcf//`
+
+cat $1 | grep "^#" > $bname.sorted.vcf
+#sometimes lobSTR gives you unsorted vcf for some reason
+cat $1 | grep -v "^#" | sort -t $'\t' -k1,1 -k2,2n >> $bname.sorted.vcf
+
+bgzip $bname.sorted.vcf 
+tabix $bname.sorted.vcf.gz 
+
+#there may be no gene
+vcfanno -base-path ~/cre/ ~/cre/cre.annotate_str.toml $bname.sorted.vcf.gz > $bname.annotated.vcf
+rm $bname.insertions.txt
+echo -e "CHR\tPOS\tREF\tALT\tGENE\tGENOTYPE\tINSERTION_LENGTH_BP" > $bname.insertions.txt
+cat $bname.annotated.vcf | grep -v "^#" | sed s/"gene="/"\t"/g | grep "0/1:" | awk '{print $1"\t"$2"\t"$4"\t"$5"\t"$9"\t"$NF}' | sed s/":.*"// | \
+    awk '{if (length($3)<length($4)) print $0"\t"length($4)-length($3);}' | sort -k7,7 -rn >> $bname.insertions.txt

cre.annotate_str.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="protein_coding_genes.bed.gz"
+columns = [4]
+names=["gene"]
+ops=["self"]