broadinstitute · nikellepetrillo · Mar 9, 2026 · Feb 27, 2026 · Feb 27, 2026 · Feb 27, 2026
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -4,11 +4,11 @@ workflows:
   - name: aggregate_rsem_results
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/aggregate_rsem_results.wdl
- 
+
   - name: AggregateSusieWorkflow
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/AggregateSusieWorkflow.wdl
- 
+
   - name: ArrayImputationQuotaConsumed
     subclass: WDL
     primaryDescriptorPath: /pipelines/wdl/arrays/imputation_beagle/ArrayImputationQuotaConsumed.wdl
@@ -25,19 +25,19 @@ workflows:
   - name: Beagle5Phasing
     subclass: WDL
     primaryDescriptorPath: /all_of_us/phasing/Beagle5Phasing.wdl
-  
+
   - name: BuildIndices
     subclass: WDL
     primaryDescriptorPath: /pipelines/wdl/build_indices/BuildIndices.wdl
 
   - name: CalculatePhenotypeGroups
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/CalculatePhenotypeGroups.wdl
-  
+
   - name: convert_vcf_to_plink_bed
     subclass: WDL
     primaryDescriptorPath: /all_of_us/admixture/convert_vcf_to_plink_bed.wdl
-  
+
   - name: CramToUnmappedBams
     subclass: WDL
     primaryDescriptorPath: /pipelines/wdl/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl
@@ -66,6 +66,10 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /all_of_us/cmrg/FixItFelixAndVariantCall.wdl
 
+  - name: Glimpse2LowPassImputation
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.wdl
+
   - name: get_wgs_median_coverage
     subclass: WDL
     primaryDescriptorPath: /all_of_us/mitochondria/get_wgs_median_coverage.wdl
@@ -216,7 +220,7 @@ workflows:
   - name: SusieR_Workflow
     subclass: WDL
     primaryDescriptorPath: /all_of_us/rna_seq/susieR_workflow.wdl
-  
+
   - name: TestArrayImputationQC
     subclass: WDL
     primaryDescriptorPath: /verification/test-wdls/TestArrayImputationQC.wdl

diff --git a/all_of_us/mitochondria/mt_coverage_merge.wdl b/all_of_us/mitochondria/mt_coverage_merge.wdl
@@ -566,9 +566,11 @@ task merge_mt_shards {
 
         # Copy tarball to stable GCS location for call caching
         command -v gcloud
-                    DEST_ROOT="~{output_bucket}"
-                    DEST_ROOT="${DEST_ROOT%/}"
-                    DEST_PATH="${DEST_ROOT}/~{out_mt_name}.tar.gz"
+        # Disable parallel composite uploads so md5Hash is available.
+        gcloud config set storage/parallel_composite_upload_enabled False
+                DEST_ROOT="~{output_bucket}"
+                DEST_ROOT="${DEST_ROOT%/}"
+                DEST_PATH="${DEST_ROOT}/~{out_mt_name}.tar.gz"
         gcloud storage cp "~{out_mt_name}.tar.gz" "${DEST_PATH}"
 
         LOCAL_MD5_B64=$(python3 - <<'PY'
@@ -614,15 +616,16 @@ task finalize_mt_with_covdb {
         String artifact_prone_sites_reference = "default"
         String file_name
         Int minimum_homref_coverage = 100
-        Int homref_position_block_size = 2048
+        Int homref_position_block_size = 1024
         Int n_final_partitions = 1000
         Boolean overwrite = false
 
         # Runtime parameters
-        Int memory_gb = 256
-        Int cpu = 40
+        Int memory_gb = 768
+        Int cpu = 96
         Int disk_gb = 4000
         String disk_type = "SSD"
+        String machine_type = "n2d-highmem-96"
     }
 
     command <<<
@@ -703,6 +706,7 @@ task finalize_mt_with_covdb {
         memory: memory_gb + " GB"
         cpu: cpu
         disks: "local-disk " + disk_gb + " " + disk_type
+        predefinedMachineType: machine_type
     }
 }
 

diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -4,6 +4,7 @@ BuildIndices	 5.1.0	2026-02-13
 CramToUnmappedBams	 1.1.3	2024-08-02 
 ExomeGermlineSingleSample	 3.2.7	2026-01-21 
 ExomeReprocessing	 3.3.7	2026-01-21 
+Glimpse2LowPassImputation	 0.0.1	2026-02-26 
 IlluminaGenotypingArray	 1.12.27	2026-01-21 
 Imputation	 1.1.23	2025-10-03 
 ImputationBeagle	 3.0.1	2026-02-23 

diff --git a/...n_beagle/input_qc/test_inputs/Plumbing/HDGP1000G_500_chr20_qc_fails_no_valid_contigs.json b/...n_beagle/input_qc/test_inputs/Plumbing/HDGP1000G_500_chr20_qc_fails_no_valid_contigs.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_only_chr20.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_only_chr20.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["this_contig_is_not_in_inputs_1", "this_contig_is_not_in_inputs_2", "this_contig_is_not_in_inputs_3"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_no_valid_contigs"
 }
diff --git a/.../imputation_beagle/input_qc/test_inputs/Plumbing/HDGP1000G_500_qc_fails_not_bgzipped.json b/.../imputation_beagle/input_qc/test_inputs/Plumbing/HDGP1000G_500_qc_fails_not_bgzipped.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_not_bgzipped.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_not_bgzipped.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_not_bgzipped"
 }
diff --git a/...wdl/arrays/imputation_beagle/input_qc/test_inputs/Plumbing/HDGP1000G_500_qc_fails_v3.json b/...wdl/arrays/imputation_beagle/input_qc/test_inputs/Plumbing/HDGP1000G_500_qc_fails_v3.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_vcf_version_3.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_vcf_version_3.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_vcf_version_3"
 }
diff --git a/...rays/imputation_beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_chr20_qc_succeeds.json b/...rays/imputation_beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_chr20_qc_succeeds.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_only_chr20.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_only_chr20.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_subset_succeeds"
 }
diff --git a/...beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_qc_fails_bad_contig_header_length.json b/...beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_qc_fails_bad_contig_header_length.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_bad_contig_header_length.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_bad_contig_header_length.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_bad_contig_header_length"
 }
diff --git a/...putation_beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_qc_fails_multiple_errors.json b/...putation_beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_qc_fails_multiple_errors.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_v3_no_data_not_bgzipped.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_v3_no_data_not_bgzipped.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_multiple_errors"
 }
diff --git a/...beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_qc_fails_wrong_contig_name_header.json b/...beagle/input_qc/test_inputs/Plumbing/HGDP1000G_500_qc_fails_wrong_contig_name_header.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_wrong_contig_name_header.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_wrong_contig_name_header.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_wrong_contig_name_header"
 }
diff --git a/...ys/imputation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_bad_coded_indels.json b/...ys/imputation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_bad_coded_indels.json
@@ -1,8 +1,8 @@
 {
-  "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_bad_coded_indels.vcf.gz",
+  "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_bad_coded_indels.vcf.gz",
   "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-  "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+  "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
   "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-  "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+  "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
   "ArrayImputationQC.output_basename": "plumbing_test_fail_bad_coded_indels"
 }
diff --git a/...rrays/imputation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_bad_order_chr.json b/...rrays/imputation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_bad_order_chr.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_not_in_order_chr.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_not_in_order_chr.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_bad_order_chr"
 }
diff --git a/...rrays/imputation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_bad_order_pos.json b/...rrays/imputation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_bad_order_pos.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_not_in_order_pos.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_not_in_order_pos.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_bad_order_pos"
 }
diff --git a/...ation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_missing_length_attribute.json b/...ation_beagle/input_qc/test_inputs/Plumbing/NA12878_qc_fails_missing_length_attribute.json
@@ -1,8 +1,8 @@
 {
-  "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/test_qc_missing_length_attr.vcf.gz",
+  "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/test_qc_missing_length_attr.vcf.gz",
   "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-  "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+  "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panelhgdp.tgp.gwaspy.AN_added.bcf.ac2",
   "ArrayImputationQC.contigs": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
-  "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+  "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
   "ArrayImputationQC.output_basename": "plumbing_test_fail_missing_length_attribute"
 }
diff --git a/...ion_beagle/input_qc/test_inputs/Plumbing/NA12878_wgs_chr20_qc_fails_too_many_records.json b/...ion_beagle/input_qc/test_inputs/Plumbing/NA12878_wgs_chr20_qc_fails_too_many_records.json
@@ -1,8 +1,8 @@
 {
-    "ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/NA12878.annotated.chr20_over_three_million_sites.g.vcf.gz",
+    "ArrayImputationQC.multi_sample_vcf": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/vcfs/NA12878.annotated.chr20_over_three_million_sites.g.vcf.gz",
     "ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-    "ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
+    "ArrayImputationQC.reference_panel_path_prefix": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
     "ArrayImputationQC.contigs": ["this_contig_is_not_in_inputs_1", "this_contig_is_not_in_inputs_2", "this_contig_is_not_in_inputs_3"],
-    "ArrayImputationQC.genetic_maps_path": "gs://broad-gotc-test-storage/imputation_beagle/scientific/plink-genetic-maps/",
+    "ArrayImputationQC.genetic_maps_path": "gs://pd-test-storage-public/ArrayImputationQC/input/plumbing/plink-genetic-maps/",
     "ArrayImputationQC.output_basename": "plumbing_test_fail_too_many_records"
 }