From 7954f36af5159bb09d629c3589dbcf7c5e80c7f2 Mon Sep 17 00:00:00 2001
From: asylvz <asoylev@gmail.com>
Date: Thu, 15 Aug 2019 14:54:37 +0300
Subject: [PATCH] Modified ALT fields in VCF header

---
 variants.c | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/variants.c b/variants.c
index a3f8ace..cd0c336 100644
--- a/variants.c
+++ b/variants.c
@@ -573,7 +573,14 @@ void print_vcf_header( FILE *fpOut, bam_info** in_bams, parameters *params)
 			"##FORMAT=<ID=RP,Number=1,Type=Integer,Description=\"Read Pair Support\">\n"
 			"##FORMAT=<ID=SR,Number=1,Type=Integer,Description=\"Split Read Support\">\n";
 
-	char header_alt[]="##ALT=<ID=DEL,Description=\"Deletion\">\n";
+	char header_alt[]="##ALT=<ID=DEL,Description=\"Deletion\">\n"
+			"##ALT=<ID=DEL:ME,Description=\"Deletion of mobile element\">\n"
+			"##ALT=<ID=INS,Description=\"Novel sequence insertion\">\n"
+			"##ALT=<ID=INS:ME,Description=\"Mobile element insertion\">\n"
+			"##ALT=<ID=MT,Description=\"Nuclear mitochondrial insertion\">\n"
+			"##ALT=<ID=DUP:TANDEM,Description=\"Tandem duplication\">\n"
+			"##ALT=<ID=DUP:ISP,Description=\"Interspersed duplication\">\n"
+			"##ALT=<ID=INV,Description=\"Inversion\">\n";
 	time_t rawtime;
 	struct tm * timeinfo;