From 5322038a40f0824d8537440210b14c8bdc11caeb Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 14 Jun 2022 08:26:01 -0700
Subject: [PATCH] handle iupac ambiguity codes as well as dup alleles in
 vardict

---
 callers/vardict | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/callers/vardict b/callers/vardict
index 460985c..da991c4 100755
--- a/callers/vardict
+++ b/callers/vardict
@@ -15,6 +15,6 @@ samp="$5"
 
 vardict-java -G "$genome" -N "$samp" -b "$bam" -v -c 1 -S 2 -E 3 "$peaks" -VS SILENT | \
 teststrandbias.R | var2vcf_valid.pl | \
-awk -F $"\t" -v 'OFS=\t' '/^#/ || $5 !~ /<dup/' | \
+awk -F $"\t" -v 'OFS=\t' '/^#/ || $4 !~ /^(R|Y|M|W|S|K|V|H|D|B|N)$/ && $5 !~ /<dup/' | \
 bgzip > "$output_dir/vardict.vcf.gz" && \
 tabix -p vcf -f "$output_dir/vardict.vcf.gz"