diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
index fb62099e..806f6830 100644
--- a/.github/workflows/codecov.yml
+++ b/.github/workflows/codecov.yml
@@ -192,20 +192,22 @@ jobs:
         run: |
           test/scripts/hictk_balance.sh build/src/hictk/hictk hic_tools.jar
 
+          test/scripts/hictk_convert_hic2cool.sh build/src/hictk/hictk
+          test/scripts/hictk_convert_cool2hic.sh build/src/hictk/hictk hic_tools.jar
+
           test/scripts/hictk_dump_chroms.sh build/src/hictk/hictk
           test/scripts/hictk_dump_bins.sh build/src/hictk/hictk
           test/scripts/hictk_dump_resolutions.sh build/src/hictk/hictk
           test/scripts/hictk_dump_normalizations.sh build/src/hictk/hictk
           test/scripts/hictk_dump_cells.sh build/src/hictk/hictk
 
+          test/scripts/hictk_fix_mcool.sh build/src/hictk/hictk
+
           test/scripts/hictk_dump_gw.sh build/src/hictk/hictk
           test/scripts/hictk_dump_cis.sh build/src/hictk/hictk
           test/scripts/hictk_dump_trans.sh build/src/hictk/hictk
           test/scripts/hictk_dump_balanced.sh build/src/hictk/hictk
 
-          test/scripts/hictk_convert_hic2cool.sh build/src/hictk/hictk
-          test/scripts/hictk_convert_cool2hic.sh build/src/hictk/hictk hic_tools.jar
-
           test/scripts/hictk_load_coo.sh build/src/hictk/hictk sorted
           test/scripts/hictk_load_coo.sh build/src/hictk/hictk unsorted
           test/scripts/hictk_load_bg2.sh build/src/hictk/hictk sorted
diff --git a/.github/workflows/macos-ci.yml b/.github/workflows/macos-ci.yml
index 5c8a0857..9dcbcc06 100644
--- a/.github/workflows/macos-ci.yml
+++ b/.github/workflows/macos-ci.yml
@@ -366,6 +366,14 @@ jobs:
         run: |
           test/scripts/hictk_balance.sh bin/hictk hic_tools.jar
 
+      - name: Test hictk convert (hic2cool)
+        run: |
+          test/scripts/hictk_convert_hic2cool.sh bin/hictk
+
+      - name: Test hictk convert (cool2hic)
+        run: |
+          test/scripts/hictk_convert_cool2hic.sh bin/hictk hic_tools.jar
+
       - name: Test hictk dump chroms
         run: |
           test/scripts/hictk_dump_chroms.sh bin/hictk
@@ -402,13 +410,9 @@ jobs:
         run: |
           test/scripts/hictk_dump_balanced.sh bin/hictk
 
-      - name: Test hictk convert (hic2cool)
+      - name: Test hictk fix-mcool
         run: |
-          test/scripts/hictk_convert_hic2cool.sh bin/hictk
-
-      - name: Test hictk convert (cool2hic)
-        run: |
-          test/scripts/hictk_convert_cool2hic.sh bin/hictk hic_tools.jar
+          test/scripts/hictk_fix_mcool.sh bin/hictk
 
       - name: Test hictk load coo sorted
         run: |
diff --git a/.github/workflows/ubuntu-ci.yml b/.github/workflows/ubuntu-ci.yml
index 17953490..329d7ecb 100644
--- a/.github/workflows/ubuntu-ci.yml
+++ b/.github/workflows/ubuntu-ci.yml
@@ -419,6 +419,14 @@ jobs:
         run: |
           test/scripts/hictk_balance.sh bin/hictk hic_tools.jar
 
+      - name: Test hictk convert (hic2cool)
+        run: |
+          test/scripts/hictk_convert_hic2cool.sh bin/hictk
+
+      - name: Test hictk convert (cool2hic)
+        run: |
+          test/scripts/hictk_convert_cool2hic.sh bin/hictk hic_tools.jar
+
       - name: Test hictk dump chroms
         run: |
           test/scripts/hictk_dump_chroms.sh bin/hictk
@@ -455,13 +463,9 @@ jobs:
         run: |
           test/scripts/hictk_dump_balanced.sh bin/hictk
 
-      - name: Test hictk convert (hic2cool)
+      - name: Test hictk fix-mcool
         run: |
-          test/scripts/hictk_convert_hic2cool.sh bin/hictk
-
-      - name: Test hictk convert (cool2hic)
-        run: |
-          test/scripts/hictk_convert_cool2hic.sh bin/hictk hic_tools.jar
+          test/scripts/hictk_fix_mcool.sh bin/hictk
 
       - name: Test hictk load coo sorted
         run: |
diff --git a/cmake/FetchTestDataset.cmake b/cmake/FetchTestDataset.cmake
index 856a3b9d..e01c0c39 100644
--- a/cmake/FetchTestDataset.cmake
+++ b/cmake/FetchTestDataset.cmake
@@ -4,8 +4,8 @@
 
 # cmake-format: off
 file(
-  DOWNLOAD https://zenodo.org/record/8386066/files/hictk_test_data.tar.xz?download=1
-  EXPECTED_HASH SHA256=77e2b9186d9edb90a8436fc41d6c0632727df3af95acb74e9635d1c0f29f2b8d
+  DOWNLOAD https://zenodo.org/record/8392109/files/hictk_test_data.tar.xz?download=1
+  EXPECTED_HASH SHA256=43d05077082603cf03dc5ce2bfc0f81b2422c7249ee987e09512d2e3a56afff1
   "${PROJECT_SOURCE_DIR}/test/data/hictk_test_data.tar.xz")
 # cmake-format: on
 
diff --git a/test/scripts/hictk_fix_mcool.sh b/test/scripts/hictk_fix_mcool.sh
new file mode 100755
index 00000000..06c81aea
--- /dev/null
+++ b/test/scripts/hictk_fix_mcool.sh
@@ -0,0 +1,73 @@
+#!/usr/bin/env bash
+
+# Copyright (C) 2023 Roberto Rossini <roberros@uio.no>
+#
+# SPDX-License-Identifier: MIT
+
+set -e
+set -o pipefail
+set -u
+
+echo "#########################"
+echo "#### hictk fix-mcool ####"
+
+# readlink -f is not available on macos...
+function readlink_py {
+  set -eu
+  python3 -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' "$1"
+}
+
+function check_files_exist {
+  set -eu
+  status=0
+  for f in "$@"; do
+    if [ ! -f "$f" ]; then
+      2>&1 echo "Unable to find test file \"$f\""
+      status=1
+    fi
+  done
+
+  return "$status"
+}
+
+status=0
+
+if [ $# -ne 1 ]; then
+  2>&1 echo "Usage: $0 path_to_hictk"
+  status=1
+fi
+
+hictk_bin="$1"
+
+data_dir="$(readlink_py "$(dirname "$0")/../data/")"
+script_dir="$(readlink_py "$(dirname "$0")")"
+
+invalid_mcool="$data_dir/cooler/invalid_coolers/corrupted_index.mcool"
+
+export PATH="$PATH:$script_dir"
+
+if [ $status -ne 0 ]; then
+  exit $status
+fi
+
+if ! check_files_exist "$invalid_mcool"; then
+  exit 1
+fi
+
+outdir="$(mktemp -d -t hictk-tmp-XXXXXXXXXX)"
+trap 'rm -rf -- "$outdir"' EXIT
+
+"$hictk_bin" fix-mcool "$invalid_mcool" "$outdir/out.mcool"
+
+if ! "$hictk_bin" validate --validate-index "$outdir/out.mcool"; then
+  status=1
+fi
+
+if [ "$status" -eq 0 ]; then
+  printf '\n### PASS ###\n'
+else
+  cat "$outdir/out.txt"
+  printf '\n### FAIL ###\n'
+fi
+
+exit "$status"
diff --git a/test/scripts/hictk_validate.sh b/test/scripts/hictk_validate.sh
index c03cdf5d..da139649 100755
--- a/test/scripts/hictk_validate.sh
+++ b/test/scripts/hictk_validate.sh
@@ -46,7 +46,7 @@ valid_hic="$data_dir/hic/4DNFIZ1ZVXC8.hic8"
 valid_cooler="$data_dir/cooler/ENCFF993FGR.2500000.cool"
 valid_mcool="$data_dir/cooler/multires_cooler_test_file.mcool"
 valid_scool="$data_dir/cooler/single_cell_cooler_test_file.scool"
-invalid_cooler="$data_dir/cooler/invalid_coolers/4DNFI9GMP2J8.1000000.cool"
+invalid_cooler="$data_dir/cooler/invalid_coolers/corrupted_index.mcool::/resolutions/10000000"
 
 export PATH="$PATH:$script_dir"
 
diff --git a/test/units/cooler/utils_validation_test.cpp b/test/units/cooler/utils_validation_test.cpp
index 33b40c40..87ab082a 100644
--- a/test/units/cooler/utils_validation_test.cpp
+++ b/test/units/cooler/utils_validation_test.cpp
@@ -118,8 +118,14 @@ TEST_CASE("Cooler: index validation", "[cooler][short]") {
     CHECK(cooler::utils::index_is_valid(path2.string()));
   }
   SECTION("broken index") {
-    const auto path = datadir / "invalid_coolers/4DNFI9GMP2J8.1000000.cool";
-    CHECK_FALSE(cooler::utils::index_is_valid(path.string()));
+    SECTION(".cool") {
+      const auto path = datadir / "invalid_coolers/corrupted_index.mcool::/resolutions/10000000";
+      CHECK_FALSE(cooler::utils::index_is_valid(path.string()));
+    }
+    SECTION(".mcool") {
+      const auto path = datadir / "invalid_coolers/corrupted_index.mcool";
+      CHECK_FALSE(cooler::utils::index_is_valid(path.string()));
+    }
   }
 }