Merge branch 'develop' into rc-2356-shardids

jiveshs98 · Feb 15, 2024 · c4f0f39 · c4f0f39
2 parents b38afe7 + 69c6827
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diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md
@@ -1,3 +1,9 @@
+# 1.6.9
+2023-09-08 (Date of Last Commit)
+
+* Added option to run VETS instead of VQSR for filtering
+* Added option to hard filter sites outside of provided interval list
+
 # 1.6.8
 2023-06-29 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
diff --git a/...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md b/...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md
@@ -1,3 +1,13 @@
+# 1.1.6
+2023-02-06 (Date of Last Commit)
+
+* Updated VETS filtering pipeline to GATK version 4.5.0.0. Does not affect outputs.
+
+# 1.1.5
+2023-09-08 (Date of Last Commit)
+
+* Added option to hard filter sites outside of provided interval list to HardFilterAndMakeSitesOnlyVcf task
+
 # 1.1.4
 2023-06-29 (Date of Last Commit)
 

diff --git a/.../broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl b/.../broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl
@@ -1,7 +1,7 @@
 version 1.0
 
 import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
-import "https://raw.githubusercontent.com/broadinstitute/gatk/4.3.0.0/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl" as Filtering
+import "https://raw.githubusercontent.com/broadinstitute/gatk/4.5.0.0/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl" as Filtering
 import "../../../../../../tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" as FilteringThreshold
 
 
@@ -11,7 +11,7 @@ import "../../../../../../tasks/broad/UltimaGenomicsGermlineFilteringThreshold.w
 # For choosing a filtering threshold (where on the ROC curve to filter) a sample with truth data is required.
 workflow UltimaGenomicsJointGenotyping {
 
-  String pipeline_version = "1.1.4"
+  String pipeline_version = "1.1.6"
 
   input {
     File unpadded_intervals_file
@@ -51,10 +51,11 @@ workflow UltimaGenomicsJointGenotyping {
     String flow_order
 
     #inputs for training and applying filter model
-    String snp_annotations
-    String indel_annotations
-    Boolean use_allele_specific_annotations
+    Array[String] snp_annotations
+    Array[String] indel_annotations
     String model_backend
+    String snp_resource_args = "--resource:hapmap,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz --resource:omni,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz --resource:1000G,training=true,calibration=false gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
+    String indel_resource_args = "--resource:mills,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
 
     Int? top_level_scatter_count
     Boolean? gather_vcfs
@@ -154,24 +155,42 @@ workflow UltimaGenomicsJointGenotyping {
       disk_size_gb = medium_disk
   }
 
-  call Filtering.JointVcfFiltering as TrainAndApplyFilteringModel {
+  call Filtering.JointVcfFiltering as TrainAndApplyFilteringModelSNPs {
     input:
-      vcf = CalculateAverageAnnotations.output_vcf,
-      vcf_index = CalculateAverageAnnotations.output_vcf_index,
+      input_vcfs = CalculateAverageAnnotations.output_vcf,
+      input_vcf_idxs = CalculateAverageAnnotations.output_vcf_index,
       sites_only_vcf = SitesOnlyGatherVcf.output_vcf,
-      sites_only_vcf_index = SitesOnlyGatherVcf.output_vcf_index,
-      snp_annotations = snp_annotations,
-      indel_annotations = indel_annotations,
+      sites_only_vcf_idx = SitesOnlyGatherVcf.output_vcf_index,
+      annotations = snp_annotations,
+      resource_args = snp_resource_args,
       model_backend = model_backend,
-      use_allele_specific_annotations = use_allele_specific_annotations,
-      basename = callset_name,
-      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
+      output_prefix = callset_name,
+      extract_extra_args = "--mode SNP",
+      train_extra_args = "--mode SNP",
+      score_extra_args = "--mode SNP",
+      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
+  }
+
+  call Filtering.JointVcfFiltering as TrainAndApplyFilteringModelINDELs {
+    input:
+      input_vcfs = TrainAndApplyFilteringModelSNPs.scored_vcfs,
+      input_vcf_idxs = TrainAndApplyFilteringModelSNPs.scored_vcf_idxs,
+      sites_only_vcf = SitesOnlyGatherVcf.output_vcf,
+      sites_only_vcf_idx = SitesOnlyGatherVcf.output_vcf_index,
+      annotations = indel_annotations,
+      resource_args = indel_resource_args,
+      model_backend = model_backend,
+      output_prefix = callset_name,
+      extract_extra_args = "--mode INDEL",
+      train_extra_args = "--mode INDEL",
+      score_extra_args = "--mode INDEL",
+      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
   }
 
   call FilteringThreshold.ExtractOptimizeSingleSample as FindFilteringThresholdAndFilter {
     input:
-      input_vcf = TrainAndApplyFilteringModel.variant_scored_vcf,
-      input_vcf_index = TrainAndApplyFilteringModel.variant_scored_vcf_index,
+      input_vcf = TrainAndApplyFilteringModelINDELs.scored_vcfs,
+      input_vcf_index = TrainAndApplyFilteringModelINDELs.scored_vcf_idxs,
       base_file_name = callset_name,
       call_sample_name = call_sample_name,
       truth_vcf = truth_vcf,
@@ -188,7 +207,7 @@ workflow UltimaGenomicsJointGenotyping {
       medium_disk = medium_disk
   }
 
-  scatter (idx in range(length(TrainAndApplyFilteringModel.variant_scored_vcf))) {
+  scatter (idx in range(length(TrainAndApplyFilteringModelINDELs.scored_vcfs))) {
     # For large callsets we need to collect metrics from the shards and gather them later.
     if (!is_small_callset) {
       call Tasks.CollectVariantCallingMetrics as CollectMetricsSharded {

diff --git a/...na_seq/germline/joint_genotyping/UltimaGenomics/test_inputs/Plumbing/plumbing.inputs.json b/...na_seq/germline/joint_genotyping/UltimaGenomics/test_inputs/Plumbing/plumbing.inputs.json
@@ -14,17 +14,17 @@
 "UltimaGenomicsJointGenotyping.scatter_cross_check_fingerprints":false,
 "UltimaGenomicsJointGenotyping.unbounded_scatter_count_scale_factor":2.5,
 "UltimaGenomicsJointGenotyping.unpadded_intervals_file":"gs://gcp-public-data--broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
-"UltimaGenomicsJointGenotyping.snp_annotations": "-A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE -A AVERAGE_ASSEMBLED_HAPS -A AVERAGE_FILTERED_HAPS",
-"UltimaGenomicsJointGenotyping.indel_annotations": "-A AS_MQRankSum -A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE",
+"UltimaGenomicsJointGenotyping.snp_annotations": ["AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE", "AVERAGE_ASSEMBLED_HAPS", "AVERAGE_FILTERED_HAPS"],
+"UltimaGenomicsJointGenotyping.indel_annotations": ["AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE"],
 "UltimaGenomicsJointGenotyping.flow_order": "TGCA",
 "UltimaGenomicsJointGenotyping.ref_fasta_sdf": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/reference_sdf.tar",
 "UltimaGenomicsJointGenotyping.runs_file": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/runs.conservative.bed",
 "UltimaGenomicsJointGenotyping.annotation_intervals": ["gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/LCR-hs38.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/mappability.0.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/exome.twist.bed"],
-"UltimaGenomicsJointGenotyping.use_allele_specific_annotations": true,
 "UltimaGenomicsJointGenotyping.truth_vcf":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_vcf_index":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_highconf_intervals": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed",
 "UltimaGenomicsJointGenotyping.call_sample_name": "NA12878",
 "UltimaGenomicsJointGenotyping.truth_sample_name": "HG001",
-"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST"
+"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST",
+"UltimaGenomicsJointGenotyping.TrainAndApplyFilteringModelSNPs.train_runtime_attributes": {"additional_mem_gb":2}
 }
diff --git a/...eq/germline/joint_genotyping/UltimaGenomics/test_inputs/Scientific/scientific.inputs.json b/...eq/germline/joint_genotyping/UltimaGenomics/test_inputs/Scientific/scientific.inputs.json
@@ -14,17 +14,18 @@
 "UltimaGenomicsJointGenotyping.scatter_cross_check_fingerprints":false,
 "UltimaGenomicsJointGenotyping.unbounded_scatter_count_scale_factor":2.5,
 "UltimaGenomicsJointGenotyping.unpadded_intervals_file":"gs://gcp-public-data--broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
-"UltimaGenomicsJointGenotyping.snp_annotations": "-A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE -A AVERAGE_ASSEMBLED_HAPS -A AVERAGE_FILTERED_HAPS",
-"UltimaGenomicsJointGenotyping.indel_annotations": "-A AS_MQRankSum -A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE",
+"UltimaGenomicsJointGenotyping.snp_annotations": ["AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE", "AVERAGE_ASSEMBLED_HAPS", "AVERAGE_FILTERED_HAPS"],
+"UltimaGenomicsJointGenotyping.indel_annotations": ["AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE"],
 "UltimaGenomicsJointGenotyping.flow_order": "TGCA",
 "UltimaGenomicsJointGenotyping.ref_fasta_sdf": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/reference_sdf.tar",
 "UltimaGenomicsJointGenotyping.runs_file": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/runs.conservative.bed",
 "UltimaGenomicsJointGenotyping.annotation_intervals": ["gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/LCR-hs38.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/mappability.0.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/exome.twist.bed"],
-"UltimaGenomicsJointGenotyping.use_allele_specific_annotations": true,
 "UltimaGenomicsJointGenotyping.truth_vcf":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_vcf_index":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_highconf_intervals": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed",
 "UltimaGenomicsJointGenotyping.call_sample_name": "NA12878",
 "UltimaGenomicsJointGenotyping.truth_sample_name": "HG001",
-"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST"
+"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST",
+"UltimaGenomicsJointGenotyping.TrainAndApplyFilteringModelSNPs.extract_runtime_attributes": {"command_mem_gb":13, "additional_mem_gb":2},
+"UltimaGenomicsJointGenotyping.TrainAndApplyFilteringModelSNPs.train_runtime_attributes": {"command_mem_gb":13, "additional_mem_gb":2}
 }
diff --git a/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md
@@ -1,3 +1,8 @@
+# 1.4.11
+2023-09-08 (Date of Last Commit)
+
+* Added option to hard filter sites outside of provided interval list to HardFilterAndMakeSitesOnlyVcf task
+
 # 1.4.10
 2023-06-29 (Date of Last Commit)
 

diff --git a/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl b/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl
@@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
 # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19)
 workflow JointGenotypingByChromosomePartOne {
 
-  String pipeline_version = "1.4.10"
+  String pipeline_version = "1.4.11"
 
   input {
     File unpadded_intervals_file

diff --git a/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md b/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md
@@ -1,3 +1,8 @@
+# 1.4.10
+2023-09-08 (Date of Last Commit)
+
+* Added option to hard filter sites outside of provided interval list to HardFilterAndMakeSitesOnlyVcf task
+
 # 1.4.9
 2023-06-29 (Date of Last Commit)
 

diff --git a/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl b/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl
@@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
 # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19)
 workflow JointGenotypingByChromosomePartTwo {
 
-  String pipeline_version = "1.4.9"
+  String pipeline_version = "1.4.10"
 
   input {
     String callset_name

diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/exome/JointGenotyping.inputs.json b/pipelines/broad/dna_seq/germline/joint_genotyping/exome/JointGenotyping.inputs.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 10,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",

diff --git a/...dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gather_vcfs_high_memory.json b/...dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gather_vcfs_high_memory.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 1,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",

diff --git a/.../dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gather_vcfs_low_memory.json b/.../dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gather_vcfs_low_memory.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 10,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",

diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gnarly.json b/pipelines/broad/dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gnarly.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 10,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",

diff --git a/.../dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/shard_vcfs_high_memory.json b/.../dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/shard_vcfs_high_memory.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 1,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",

diff --git a/...d/dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/shard_vcfs_low_memory.json b/...d/dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/shard_vcfs_low_memory.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 10,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",

diff --git a/...a_seq/germline/joint_genotyping/exome/test_inputs/Scientific/gather_vcfs_high_memory.json b/...a_seq/germline/joint_genotyping/exome/test_inputs/Scientific/gather_vcfs_high_memory.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 1,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",

diff --git a/...na_seq/germline/joint_genotyping/exome/test_inputs/Scientific/gather_vcfs_low_memory.json b/...na_seq/germline/joint_genotyping/exome/test_inputs/Scientific/gather_vcfs_low_memory.json
@@ -9,8 +9,8 @@
   "JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
   "JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
-  "JointGenotyping.snp_filter_level": 99.7,
-  "JointGenotyping.indel_filter_level": 95.0,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_indel_filter_level": 95.0,
   "JointGenotyping.snp_vqsr_downsampleFactor": 10,
   "JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
   "JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",