diff --git a/code/reference_data/rss_ld_sketch.ipynb b/code/reference_data/rss_ld_sketch.ipynb
index 53b626c5..c35d080f 100644
--- a/code/reference_data/rss_ld_sketch.ipynb
+++ b/code/reference_data/rss_ld_sketch.ipynb
@@ -698,7 +698,9 @@
     "# Steps per chromosome:\n",
     "#   1. For each block: plink2 --import-dosage → unsorted pgen, then --sort-vars → sorted pgen\n",
     "#   2. plink2 --pmerge-list → one per-chrom pgen\n",
-    "#   3. Clean up all intermediates including -merge.* files\n",
+    "#   3. Concatenate .afreq\n",
+    "#   4. Clean up intermediates including -merge.* files and per-block dirs\n",
+    "#   5. zstd compress final pgen/pvar/psam/afreq\n",
     "#\n",
     "# Run after process_block completes (or run together: sos run ... process_block merge_chrom)\n",
     "parameter: chrom      = 0\n",
@@ -719,7 +721,7 @@
     "_chroms = _chroms_to_process(output_dir, chrom)\n",
     "\n",
     "input: []\n",
-    "output: [f\"{output_dir}/{c}/{cohort_id}.{c}.pgen\" for c in _chroms]\n",
+    "output: [f\"{output_dir}/{c}/{cohort_id}.{c}.pgen.zst\" for c in _chroms]\n",
     "\n",
     "for _chrom in _chroms:\n",
     "    bash(f\"\"\"\n",
@@ -791,6 +793,13 @@
     "    for block_dir in \"${{chrom_dir}}\"/*/; do\n",
     "        rm -rf \"${{block_dir}}\"\n",
     "    done\n",
+    "\n",
+    "    # ── Step 5: zstd compress final outputs ──\n",
+    "    for ext in pgen pvar psam afreq; do\n",
+    "        zstd --ultra -22 -T{numThreads} \"${{final_prefix}}.${{ext}}\" \\\n",
+    "            -o \"${{final_prefix}}.${{ext}}.zst\" \\\n",
+    "            && rm -f \"${{final_prefix}}.${{ext}}\"\n",
+    "    done\n",
     "    \"\"\")"
    ]
   }