diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
index 5ed1bb5e8..22f5a0494 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
@@ -45,12 +45,17 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 			doc="used only with --somatic;  normal sample must have at least minNormalCoverage or more reads to call germline/somatic indel", required=false)
 	int minNormalCoverage = 4;
 	@Argument(fullName="minFraction", shortName="minFraction", 
-			doc="minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for a consensus call"+
+			doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for a consensus call"+
 			" (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false)
 	double minFraction = 0.3;
 	@Argument(fullName="minConsensusFraction", shortName="minConsensusFraction", 
 			doc="Minimum fraction of CONSENSUS indel observations at a site wrt all indel observations at the site required to make the call", required=false)
 	double minConsensusFraction = 0.7;
+	@Argument(fullName="minIndelCount", shortName="minCnt", 
+			doc="Minimum count of reads supporting consensus indel required for making the call. "+
+			" This filter supercedes minFraction, i.e. indels with acceptable minFraction at low coverage "+
+			"(minIndelCount not met) will not pass.", required=false)
+	int minIndelCount = 0;
 	@Argument(fullName="refseq", shortName="refseq", 
 			doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated as GENOMIC/UTR/INTRON/CODING", required=false)
 	String RefseqFileName = null;
@@ -275,13 +280,16 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 	}	
 	
 	/** Returns true if consensus (specified by the pair) should be considered a call given current values
-	 * of the fraction cutoffs
-	 * @param p
-	 * @param coverage
+	 * of the cutoffs.
+	 * @param p pair with first element being the consensus indel variant, the second element being the <i>total</i> (consensus+others)
+	 * 		count of indels at the site.
+	 * @param coverage total coverage (number of spanning reads, including those with indel(s)) at the site.
 	 * @return
 	 */
 	private boolean isCall(Pair<IndelVariant,Integer> p, int coverage) {
-		return ( (double)p.first.getCount() > minFraction * coverage && (double) p.first.getCount() > minConsensusFraction*p.second ); 		
+		return ( p.first.getCount() >= minIndelCount && 
+				(double)p.first.getCount() > minFraction * coverage && 
+				(double) p.first.getCount() > minConsensusFraction*p.second ); 		
 	}
 
 	/** Build output line for bed file and write it to the specified output writer if the latter is not null; 
@@ -502,7 +510,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 					}
 					message += "\tSOMATIC\t0/"+normal_cov;
 				} else {
-					Pair<IndelVariant,Integer> p_normal = findConsensus(tumor_variants);
+					Pair<IndelVariant,Integer> p_normal = findConsensus(normal_variants);
 					
 					message += "\tGERMLINE\t"+p_normal.second+"/"+normal_cov;
 				}