diff --git a/.lgtm.yml b/.lgtm.yml
index 3a399d4862..2619c647d4 100644
--- a/.lgtm.yml
+++ b/.lgtm.yml
@@ -16,8 +16,18 @@ extraction:
             \ | tar -xzf - --strip-components=1 -C $HOME/cmake-3.17
       - export PATH=$HOME/cmake-3.17/bin:$PATH
 
+    # Pre-analysis step.
     configure:
-      command: "./configure -cmake -opensource -confirm-license -debug -no-optimize-debug \
-        \ -nomake tests -nomake examples -no-harfbuzz -no-iconv -system-pcre -system-zlib \
-        \ -system-freetype -system-libpng -system-libjpeg -system-sqlite -- -DFEATURE_system_sqlite=ON \
-        \ -DQT_NO_MAKE_TESTS=ON -DQT_NO_MAKE_EXAMPLES=ON"
+      command:
+        - "./configure -cmake -opensource -confirm-license -debug -no-pch \
+          \ -nomake tests -nomake examples -no-harfbuzz \
+          \ -system-pcre -system-zlib -system-freetype -system-libpng \
+          \ -system-libjpeg -system-sqlite"
+        # We skip analyzing the bootstrap library, since the same code is
+        # built with non-standard flags and false-positives are flagged.
+        - ninja bootstrap_tools
+
+    # Actual analysis.
+    index:
+      build_command:
+        - ninja