From 0edbe6eb3dda517f551415a397180216c8a76015 Mon Sep 17 00:00:00 2001
From: jamesnemesh <nemesh@broadinstitute.org>
Date: Mon, 9 Jan 2023 17:18:15 -0500
Subject: [PATCH] Filter out sites with symbolic alleles when filtering to
 diploid sites (#330)

---
 .../vcftools/filters/SimpleDiploidVariantContextFilter.java  | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/java/org/broadinstitute/dropseqrna/vcftools/filters/SimpleDiploidVariantContextFilter.java b/src/java/org/broadinstitute/dropseqrna/vcftools/filters/SimpleDiploidVariantContextFilter.java
index 6405662e..fec70e3a 100644
--- a/src/java/org/broadinstitute/dropseqrna/vcftools/filters/SimpleDiploidVariantContextFilter.java
+++ b/src/java/org/broadinstitute/dropseqrna/vcftools/filters/SimpleDiploidVariantContextFilter.java
@@ -103,6 +103,11 @@ public SimpleDiploidVariantContextFilter (final Iterator<VariantContext> underly
 
 	@Override
 	public boolean filterOut(final VariantContext site) {
+		// Remove variants with symbolic alleles.
+		// These would not pass the isCanonicalAllele test later.
+		if (site.hasSymbolicAlleles()) {
+			return true;
+		}
 		// if requested, filter out any "filtered" site.
 		if (filterFilterFlagedVariants && site.isFiltered()) {
 			if (verbose) log.info("Rejecting variant site filtered "+site.toStringWithoutGenotypes());