diff --git a/code/enrichment/sldsc_enrichment.ipynb b/code/enrichment/sldsc_enrichment.ipynb
index 1bf98ce85..f94d40fb5 100644
--- a/code/enrichment/sldsc_enrichment.ipynb
+++ b/code/enrichment/sldsc_enrichment.ipynb
@@ -836,12 +836,36 @@
     "\n",
     "    emit_single_local <- ${\"TRUE\" if emit_single else \"FALSE\"}\n",
     "    emit_joint_local  <- ${\"TRUE\" if emit_joint  else \"FALSE\"}\n",
+    "    use_print_snps_local <- ${\"TRUE\" if use_print_snps else \"FALSE\"}\n",
+    "    bfile_prefix         <- \"${_input[-1]:na}\"\n",
+    "\n",
+    "    # Reshape annot to match .bim panel for ldsc.py --l2 --print-snps\n",
+    "    # (drop A1/A2/MAF, expand to .bim rows filling 0, take CM from .bim).\n",
+    "    normalize_for_ldsc <- function(df) {\n",
+    "        if (!use_print_snps_local) return(df)\n",
+    "        df <- df[, !names(df) %in% c(\"A1\", \"A2\", \"MAF\", \"CM\"), drop = FALSE]\n",
+    "        annot_cols <- setdiff(names(df), c(\"CHR\", \"BP\", \"SNP\"))\n",
+    "        bim <- as.data.frame(fread(paste0(bfile_prefix, \".bim\"), header = FALSE,\n",
+    "                                   col.names = c(\"CHR\", \"SNP\", \"CM\", \"BP\", \"A1\", \"A2\")))\n",
+    "        bim$CHR <- as.character(bim$CHR); df$CHR <- as.character(df$CHR)\n",
+    "        idx <- match(bim$SNP, df$SNP)\n",
+    "        out <- data.frame(CHR = bim$CHR, BP = bim$BP, SNP = bim$SNP, CM = bim$CM,\n",
+    "                          stringsAsFactors = FALSE)\n",
+    "        for (col in annot_cols) {\n",
+    "            v <- rep(0, nrow(bim))\n",
+    "            non_na <- !is.na(idx)\n",
+    "            v[non_na] <- df[[col]][idx[non_na]]\n",
+    "            out[[col]] <- v\n",
+    "        }\n",
+    "        out\n",
+    "    }\n",
     "\n",
     "    # ---- Write N single-target .annot files (when requested) ----\n",
     "    if (emit_single_local) {\n",
     "        for (i in seq_len(N_local)) {\n",
     "            out_anno <- ref_anno\n",
     "            out_anno$ANNOT <- score_list[[i]]\n",
+    "            out_anno <- normalize_for_ldsc(out_anno)\n",
     "            name <- paste0(\"${annotation_name}\", \"_single_\", i)\n",
     "            out_path_gz  <- file.path(\"${cwd:a}\", name, paste0(name, \".${input_chroms[_index]}.annot.gz\"))\n",
     "            out_path_tsv <- sub(\"\\\\.gz$\", \"\", out_path_gz)\n",
@@ -856,6 +880,7 @@
     "        for (i in seq_len(N_local)) {\n",
     "            joint_anno[[paste0(\"ANNOT_\", i)]] <- score_list[[i]]\n",
     "        }\n",
+    "        joint_anno <- normalize_for_ldsc(joint_anno)\n",
     "        joint_name   <- paste0(\"${annotation_name}\", \"_joint\")\n",
     "        joint_out_gz <- file.path(\"${cwd:a}\", joint_name, paste0(joint_name, \".${input_chroms[_index]}.annot.gz\"))\n",
     "        joint_out_tsv <- sub(\"\\\\.gz$\", \"\", joint_out_gz)\n",
@@ -1231,10 +1256,15 @@
     "\n",
     "    subset_per_trait <- res$per_trait[subset_traits]\n",
     "\n",
+    "    # Map wide names (tau_star_single/joint) to bare names meta_sldsc_random expects.\n",
+    "    view_single <- pecotmr:::.sldsc_view_for_meta(subset_per_trait, \"single\")\n",
+    "    view_joint  <- pecotmr:::.sldsc_view_for_meta(subset_per_trait, \"joint\")\n",
+    "\n",
     "    out <- list(\n",
-    "        tau_star   = setNames(lapply(target_cats, function(c) meta_sldsc_random(subset_per_trait, c, \"tau_star\")),   target_cats),\n",
-    "        enrichment = setNames(lapply(target_cats, function(c) meta_sldsc_random(subset_per_trait, c, \"enrichment\")), target_cats),\n",
-    "        enrichstat = setNames(lapply(target_cats, function(c) meta_sldsc_random(subset_per_trait, c, \"enrichstat\")), target_cats)\n",
+    "        tau_star_single = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_single, c, \"tau_star\")),   target_cats),\n",
+    "        tau_star_joint  = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_joint,  c, \"tau_star\")),   target_cats),\n",
+    "        enrichment      = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_single, c, \"enrichment\")), target_cats),\n",
+    "        enrichstat      = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_single, c, \"enrichstat\")), target_cats)\n",
     "    )\n",
     "\n",
     "    saveRDS(out, \"${_output[0]}\")\n",