diff --git a/Cargo.lock b/Cargo.lock
index ce6f0274..9043c325 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1476,29 +1476,6 @@ dependencies = [
  "vector_utils 0.1.5 (registry+https://github.com/rust-lang/crates.io-index)",
 ]
 
-[[package]]
-name = "vdj_ann"
-version = "0.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bf2382451427e4e963c910f39d8823ea29d015c5d77193db2aa4278c429a9dc8"
-dependencies = [
- "align_tools 0.1.11 (registry+https://github.com/rust-lang/crates.io-index)",
- "amino 0.1.7 (registry+https://github.com/rust-lang/crates.io-index)",
- "bio_edit",
- "debruijn",
- "fasta_tools 0.1.7 (registry+https://github.com/rust-lang/crates.io-index)",
- "hyperbase 0.1.8 (registry+https://github.com/rust-lang/crates.io-index)",
- "io_utils 0.3.2 (registry+https://github.com/rust-lang/crates.io-index)",
- "itertools",
- "kmer_lookup 0.1.5 (registry+https://github.com/rust-lang/crates.io-index)",
- "serde",
- "serde_json",
- "stats_utils 0.1.3 (registry+https://github.com/rust-lang/crates.io-index)",
- "string_utils 0.1.4 (registry+https://github.com/rust-lang/crates.io-index)",
- "vdj_types 0.2.0 (registry+https://github.com/rust-lang/crates.io-index)",
- "vector_utils 0.1.5 (registry+https://github.com/rust-lang/crates.io-index)",
-]
-
 [[package]]
 name = "vdj_ann_ref"
 version = "0.2.0"
@@ -1512,7 +1489,7 @@ dependencies = [
  "pretty_trace 0.5.23 (registry+https://github.com/rust-lang/crates.io-index)",
  "sha2",
  "string_utils 0.1.4 (registry+https://github.com/rust-lang/crates.io-index)",
- "vdj_ann 0.4.0 (registry+https://github.com/rust-lang/crates.io-index)",
+ "vdj_ann",
  "vector_utils 0.1.5 (registry+https://github.com/rust-lang/crates.io-index)",
 ]
 
diff --git a/vdj_ann/src/annotate.rs b/vdj_ann/src/annotate.rs
index 58c1ad33..6cdbce32 100644
--- a/vdj_ann/src/annotate.rs
+++ b/vdj_ann/src/annotate.rs
@@ -159,6 +159,7 @@ pub fn annotate_seq(
     allow_weak: bool,
     allow_improper: bool,
     abut: bool,
+    is_gd: Option<bool>, // is gamma/delta mode
 ) {
     let mut log = Vec::<u8>::new();
     annotate_seq_core(
@@ -170,6 +171,7 @@ pub fn annotate_seq(
         abut,
         &mut log,
         false,
+        is_gd,
     );
 }
 
@@ -200,6 +202,7 @@ pub fn annotate_seq_core(
     abut: bool,
     log: &mut Vec<u8>,
     verbose: bool,
+    is_gd: Option<bool>, // is gamma/delta mode
 ) {
     // The DNA string representation is inefficient because it stores bases as packed k-mers
     // which requires a lot of array bounds checks when unpacking which was a hot path
@@ -218,6 +221,8 @@ pub fn annotate_seq_core(
     const MIN_PERF_EXT: usize = 5;
     const MAX_RATE: f64 = 0.15;
 
+    // Unwrap gamma/delta mode flag
+    let gd_mode = is_gd.unwrap_or(false);
     // Find maximal perfect matches of length >= 20, or 12 for J regions, so long
     // as we have extension to a 20-mer with only one mismatch.
 
@@ -1470,7 +1475,7 @@ pub fn annotate_seq_core(
     }
     erase_if(&mut annx, &to_delete);
 
-    // For IGH and TRB, if there is a V and J, but no D, look for a D that matches nearly perfectly
+    // For IGH, TRB and TRD in gd_mode, if there is a V and J, but no D, look for a D that matches nearly perfectly
     // between them.  We consider only alignments having no indels.  The following conditions
     // are required:
     // 1. At most three mismatches.
@@ -1486,7 +1491,8 @@ pub fn annotate_seq_core(
         let t = ann.2 as usize;
         if !rheaders[t].contains("segment") {
             let rt = refdata.rtype[t];
-            if rt == 0 || rt == 4 {
+            // IGH, TRB, or TRD in gd_mode
+            if rt == 0 || rt == 4 || (gd_mode && rt == 5) {
                 if refdata.segtype[t] == "V" {
                     v = true;
                     vstop = ann.0 + ann.1;
@@ -2078,6 +2084,7 @@ pub fn print_annotations(
     allow_improper: bool,
     abut: bool,
     verbose: bool,
+    is_gd: Option<bool>, // is gamma/delta mode
 ) {
     let mut ann = Vec::<(i32, i32, i32, i32, i32)>::new();
     annotate_seq_core(
@@ -2089,6 +2096,7 @@ pub fn print_annotations(
         abut,
         log,
         verbose,
+        is_gd,
     );
     print_some_annotations(refdata, &ann, log, verbose);
 }
@@ -2717,7 +2725,7 @@ impl ContigAnnotation {
         is_gd: Option<bool>,                     // is gamma/delta mode
     ) -> ContigAnnotation {
         let mut ann = Vec::<(i32, i32, i32, i32, i32)>::new();
-        annotate_seq(b, refdata, &mut ann, true, false, true);
+        annotate_seq(b, refdata, &mut ann, true, false, true, is_gd);
         let mut log = Vec::<u8>::new();
         let productive = is_valid(b, refdata, &ann, false, &mut log, is_gd);
         ContigAnnotation::from_annotate_seq(
diff --git a/vdj_ann_ref/Cargo.toml b/vdj_ann_ref/Cargo.toml
index 525a90ae..8dce3608 100644
--- a/vdj_ann_ref/Cargo.toml
+++ b/vdj_ann_ref/Cargo.toml
@@ -21,4 +21,4 @@ pretty_trace = "0.5"
 sha2 = ">=0.9.3, <0.11"
 string_utils = "0.1"
 vector_utils = "0.1"
-vdj_ann = "0.4"
+vdj_ann = { path = "../vdj_ann" }
diff --git a/vdj_ann_ref/src/lib.rs b/vdj_ann_ref/src/lib.rs
index 20ac6be9..1fde3a98 100644
--- a/vdj_ann_ref/src/lib.rs
+++ b/vdj_ann_ref/src/lib.rs
@@ -122,7 +122,7 @@ mod tests {
         let mut refdata = RefData::new();
         make_vdj_ref_data_core(&mut refdata, refx, &ext_refx, is_tcr, is_bcr, None);
         let mut ann = Vec::<(i32, i32, i32, i32, i32)>::new();
-        annotate_seq(&seq, &refdata, &mut ann, true, false, true);
+        annotate_seq(&seq, &refdata, &mut ann, true, false, true, None);
         let mut have_d = false;
         for i in 0..ann.len() {
             if refdata.is_d(ann[i].2 as usize) {