diff --git a/.azure-pipelines.yml b/.azure-pipelines.yml
index d4ffcb60c..6c71a8080 100644
--- a/.azure-pipelines.yml
+++ b/.azure-pipelines.yml
@@ -54,81 +54,3 @@ stages:
               test_cmd: -c "import tiledbvcf; print(tiledbvcf.version)"
         steps:
         - template: ci/build-images.yml
-
-  - stage: BuildNativeLibs
-    condition: or(eq(variables.isMain, true), eq(variables.isRefTag, true))
-    jobs:
-      - job: Linux_OSX
-        strategy:
-          matrix:
-            linux:
-              imageName: 'ubuntu-24.04'
-              python.version: '3.x'
-              CXX: g++
-              BUILD_PYTHON_API: ON
-            mac:
-              imageName: 'macOS-13'
-              python.version: '3.7'
-              CXX: clang++
-              BUILD_PYTHON_API: ON
-              #SDKROOT: '/Applications/Xcode_10.3.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk'
-              MACOSX_DEPLOYMENT_TARGET: '11'
-
-        pool:
-          vmImage: $(imageName)
-        steps:
-          - task: UsePythonVersion@0
-            inputs:
-              versionSpec: '$(python.version)'
-              architecture: 'x64'
-          - script: printenv
-            displayName: 'Print Env'
-          - template: ci/native_libs-linux_osx.yml
-
-  - stage: GitHubRelease
-    condition: eq(variables.isRefTag, true)
-    jobs:
-      - job: All_OS
-        strategy:
-          matrix:
-            ubuntu_18:
-              imageName: 'ubuntu-24.04'
-        pool:
-          vmImage: $(imageName)
-
-        steps:
-          - download: current
-            patterns: '**/*.tar.gz'
-
-          - bash: |
-              unset SYSTEM
-              set +e
-              ci/collect-nativelibs.sh
-            displayName: 'Collect Native Libraries'
-
-          - task: ArchiveFiles@2
-            inputs:
-              rootFolderOrFile: '$(Build.BinariesDirectory)'
-              includeRootFolder: false
-              archiveType: 'tar' # Options: zip, 7z, tar, wim
-              tarCompression: 'gz' # Optional. Options: gz, bz2, xz, none
-              archiveFile: $(Build.ArtifactStagingDirectory)/tiledb-vcf-jar-$(Build.SourceBranchName).tar.gz
-              replaceExistingArchive: true
-              verbose: true # Optional
-            condition: succeeded()
-
-          - task: PublishBuildArtifacts@1
-            inputs:
-              pathtoPublish: $(Build.ArtifactStagingDirectory)/tiledb-vcf-jar-$(Build.SourceBranchName).tar.gz
-              artifactName: libraries
-            condition: succeeded()
-
-          - task: GithubRelease@0
-            displayName: 'GitHub Release'
-            inputs:
-              gitHubConnection: 'TileDB-Inc-Release'
-              repositoryName: TileDB-Inc/TileDB-VCF
-              tag: $(Build.SourceBranchName)
-              action: "edit"
-              isDraft: true
-              assets: $(Build.BinariesDirectory)/jars/*.jar
diff --git a/ci/native_libs-linux_osx.yml b/ci/native_libs-linux_osx.yml
deleted file mode 100755
index 4faca691a..000000000
--- a/ci/native_libs-linux_osx.yml
+++ /dev/null
@@ -1,129 +0,0 @@
-steps:
-    - bash: |
-        set -e pipefail
-
-        # Install htslib dependencies
-        if [[ "$AGENT_OS" == "Linux" ]]; then
-            sudo apt-get update && sudo apt-get install -y automake autoconf libbz2-dev liblzma-dev
-        fi
-
-        # Install bcftools (only required for running the CLI tests)
-        version=1.16
-        if [[ "$AGENT_OS" == "Linux" ]]; then
-            pushd /tmp
-            wget https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2
-            tar xfj bcftools-${version}.tar.bz2
-            cd bcftools-${version}
-            ./configure --prefix=/usr
-            make -j2
-            sudo make install
-            popd
-        else
-            brew install bcftools automake
-        fi
-
-        # Install some extra dependencies to speed up the core TileDB build
-        if [[ "$AGENT_OS" == "Linux" ]]; then
-            sudo apt-get install -y libssl-dev libbz2-dev liblz4-dev libtbb-dev libcurl4-openssl-dev zlib1g-dev
-        fi
-      displayName: 'Install dependencies'
-
-    - bash: |
-        # azure bash does not treat intermediate failure as error
-        # https://github.com/Microsoft/azure-pipelines-yaml/issues/135
-        set -e pipefail
-
-        # Azure sets "SYSTEM=build" for unknown reasons, which breaks the OpenSSL configure script (in TileDB itself)
-        #   - openssl configure uses ENV{SYSTEM} if available:
-        #     https://github.com/openssl/openssl/blob/6d745d740d37d680ff696486218b650512bbbbc6/config#L56
-        #   - error description:
-        #     https://developercommunity.visualstudio.com/content/problem/602584/openssl-build-error-when-using-pipelines.htm
-        unset SYSTEM
-
-        # Configure and build TileDB-VCF
-        mkdir -p $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build
-        cd $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build
-        cmake -DCMAKE_INSTALL_PREFIX=$BUILD_REPOSITORY_LOCALPATH/dist ..
-
-        make -j4
-        make -j4 -C libtiledbvcf tiledb_vcf_unit
-
-        make install-libtiledbvcf
-
-      displayName: 'Build and test TileDB-VCF'
-
-    - bash: |
-        set -e pipefail
-        pushd $BUILD_REPOSITORY_LOCALPATH/apis/java
-
-        ./gradlew assemble
-
-        export LD_LIBRARY_PATH=$BUILD_REPOSITORY_LOCALPATH/apis/java/build/resources/main/lib:$LD_LIBRARY_PATH
-
-      displayName: 'Build and test TileDB-VCF Java API'
-
-    - bash: |
-        echo "Testing"
-        ls
-        echo "listing JNI"
-        ls $BUILD_REPOSITORY_LOCALPATH/dist/lib
-
-        echo "listing 2"
-        ls  $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib
-
-
-        if [[ ( "$AGENT_OS" == "Linux" ) ]]; then
-          cp $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build/externals/install/lib/*.so* $BUILD_BINARIESDIRECTORY
-          cp $BUILD_REPOSITORY_LOCALPATH/dist/lib/*.so* $BUILD_BINARIESDIRECTORY
-          cp $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib/*.so* $BUILD_BINARIESDIRECTORY
-        fi
-
-        if [[ ( "$AGENT_OS" == "Darwin" ) ]]; then
-          cp $BUILD_REPOSITORY_LOCALPATH/dist/lib/*.dylib $BUILD_BINARIESDIRECTORY
-          cp $BUILD_REPOSITORY_LOCALPATH/apis/java/build/install/lib/*.dylib $BUILD_BINARIESDIRECTORY
-        fi
-
-      displayName: 'Test'
-
-    - script: |
-        echo $sourceVersion
-        commitHash=${sourceVersion:0:7}
-        echo $commitHash
-        echo "##vso[task.setvariable variable=commitHash]$commitHash" ## Set variable for using in other tasks.
-      env: { sourceVersion: $(Build.SourceVersion) }
-      displayName: Git Hash 7-digit
-
-    - bash: |
-        git describe --tags > $BUILD_REPOSITORY_LOCALPATH/version.txt
-      displayName: 'Capture version'
-
-    - task: ArchiveFiles@2
-      inputs:
-        rootFolderOrFile: '$(Build.BinariesDirectory)'
-        includeRootFolder: false
-        archiveType: 'tar' # Options: zip, 7z, tar, wim
-        tarCompression: 'gz' # Optional. Options: gz, bz2, xz, none
-        archiveFile: $(Build.ArtifactStagingDirectory)/tiledb-vcf-$(Agent.OS)-$(Build.SourceBranchName)-$(commitHash).tar.gz
-        replaceExistingArchive: true
-        verbose: true # Optional
-      condition: succeeded()
-
-    - task: PublishBuildArtifacts@1
-      inputs:
-        pathtoPublish: $(Build.ArtifactStagingDirectory)/tiledb-vcf-$(Agent.OS)-$(Build.SourceBranchName)-$(commitHash).tar.gz
-        artifactName: libraries
-      condition: succeeded()
-
-    - bash: |
-          set -e pipefail
-          # Display log files if the build failed
-          echo "Dumping log files for failed build"
-          echo "----------------------------------"
-          for f in $(find $BUILD_REPOSITORY_LOCALPATH/libtiledbvcf/build -name *.log);
-            do echo "------"
-               echo $f
-               echo "======"
-               cat $f
-            done;
-      condition: failed() # only run this job if the build step failed
-      displayName: "Print log files (failed build only)"