diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
index e106e72ac..0503e417a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
@@ -239,10 +239,10 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
         final String contig = lookupContigName(contigOffset);
         builder.chr(contig);
 
-        this.pos = decoder.decodeInt(BCF2Type.INT32);
+        this.pos = decoder.decodeInt(BCF2Type.INT32) + 1; // GATK is one based, BCF2 is zero-based
         final int refLength = decoder.decodeInt(BCF2Type.INT32);
         builder.start((long)pos);
-        builder.stop((long)(pos + refLength - 1)); // minus one because of our open intervals
+        builder.stop((long)(pos + refLength - 1)); // minus one because GATK has closed intervals but BCF2 is open
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
index e281475f2..7d9a18d14 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
@@ -84,7 +84,6 @@ import java.util.*;
  */
 class BCF2Writer extends IndexingVariantContextWriter {
     final protected static Logger logger = Logger.getLogger(BCF2Writer.class);
-    final private static List<Allele> MISSING_GENOTYPE = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
     final private static boolean ALLOW_MISSING_CONTIG_LINES = false;
 
     private final OutputStream outputStream;      // Note: do not flush until completely done writing, to avoid issues with eventual BGZF support
@@ -203,10 +202,11 @@ class BCF2Writer extends IndexingVariantContextWriter {
         // note use of encodeRawValue to not insert the typing byte
         encoder.encodeRawValue(contigIndex, BCF2Type.INT32);
 
-        // pos
-        encoder.encodeRawValue(vc.getStart(), BCF2Type.INT32);
+        // pos.  GATK is 1 based, BCF2 is 0 based
+        encoder.encodeRawValue(vc.getStart() - 1, BCF2Type.INT32);
 
-        // ref length
+        // ref length.  GATK is closed, but BCF2 is open so the ref length is GATK end - GATK start + 1
+        // for example, a SNP is in GATK at 1:10-10, which has ref length 10 - 10 + 1 = 1
         encoder.encodeRawValue(vc.getEnd() - vc.getStart() + 1, BCF2Type.INT32);
 
         // qual