BGE settings for Reblocking and JointCalling pipelines (#1076)

* reblocking changes for BGE reblocking test docker fixing TDR index issue in reblock fix the rest of the bge changes adding bge inputs fixes comment renaming inputs fix * changelogs * trying to fix tests * moving test to scientific * dragen gvcfs have a different file extension * missed one * not sure if this fixes the test because the input file is in a sample map * addressing comments * fixing bge tests * fixing tests * typo * one more * updating to gatk 4.5.0.0 * fixing vesion numbers * missed one update to 4.5.0.0 * update for new version of VETS --------- Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com>
broadinstitute · Feb 6, 2024 · 45928e3 · 45928e3
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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 +1,8 @@
+# 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
@@ -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 = "1.1.5"
 
   input {
     File unpadded_intervals_file

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",

diff --git a/...na_seq/germline/joint_genotyping/exome/test_inputs/Scientific/shard_vcfs_high_memory.json b/...na_seq/germline/joint_genotyping/exome/test_inputs/Scientific/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/...dna_seq/germline/joint_genotyping/exome/test_inputs/Scientific/shard_vcfs_low_memory.json b/...dna_seq/germline/joint_genotyping/exome/test_inputs/Scientific/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/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md b/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md
@@ -1,3 +1,10 @@
+# 2.1.10
+2023-12-14 (Date of Last Commit)
+
+* Updated GATK for Reblock task to version 4.5.0.0
+* Added options to Reblock task to remove annotations and move filters to genotype level
+
+
 # 2.1.9
 2023-12-08 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
@@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/Qc.wdl" as QC
 
 workflow ReblockGVCF {
 
-  String pipeline_version = "2.1.9"
+  String pipeline_version = "2.1.10"
 
 
   input {
@@ -17,9 +17,12 @@ workflow ReblockGVCF {
     File ref_fasta_index
     Float? tree_score_cutoff
     String? annotations_to_keep_command
+    String? annotations_to_remove_command
+    Boolean? move_filters_to_genotypes
+    String gvcf_file_extension = ".g.vcf.gz"
   }
 
-  String gvcf_basename = basename(gvcf, ".g.vcf.gz")
+  String gvcf_basename = basename(gvcf, gvcf_file_extension)
 
   call Calling.Reblock as Reblock {
     input:
@@ -30,6 +33,8 @@ workflow ReblockGVCF {
       ref_dict = ref_dict,
       tree_score_cutoff = tree_score_cutoff,
       annotations_to_keep_command = annotations_to_keep_command,
+      annotations_to_remove_command = annotations_to_remove_command,
+      move_filters_to_genotypes = move_filters_to_genotypes,
       output_vcf_filename = gvcf_basename + ".rb.g.vcf.gz"
   }
 

diff --git a/...road/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/NA12878.bge.json b/...road/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/NA12878.bge.json
@@ -0,0 +1,11 @@
+{
+  "ReblockGVCF.gvcf": "gs://broad-gotc-test-storage/ReblockGVCF/input/scientific/NA12878.bge/NA12878.hard-filtered.gvcf.gz",
+  "ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/ReblockGVCF/input/scientific/NA12878.bge/NA12878.hard-filtered.gvcf.gz.tbi",
+  "ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/bge_exome_calling_regions.v1.1.interval_list",
+  "ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
+  "ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
+  "ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "ReblockGVCF.annotations_to_remove_command": "--format-annotations-to-remove PRI",
+  "ReblockGVCF.move_filters_to_genotypes": true,
+  "ReblockGVCF.gvcf_file_extension": ".gvcf.gz"
+}
diff --git a/...broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/gather_vcfs_high_memory.json b/...broad/dna_seq/germline/joint_genotyping/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/.../broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/gather_vcfs_low_memory.json b/.../broad/dna_seq/germline/joint_genotyping/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/test_inputs/Plumbing/gnarly.json b/pipelines/broad/dna_seq/germline/joint_genotyping/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/pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/plumbing.input.json b/pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/plumbing.input.json
@@ -26,11 +26,11 @@
 
   "JointGenotyping.snp_vqsr_downsampleFactor": 10,
   "JointGenotyping.snps_variant_recalibration_threshold": 20000,
-  "JointGenotyping.snp_filter_level": 99.7,
+  "JointGenotyping.vqsr_snp_filter_level": 99.7,
   "JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"],
   "JointGenotyping.snp_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.8", "99.6", "99.5", "99.4", "99.3", "99.0", "98.0", "97.0", "90.0" ],
 
-  "JointGenotyping.indel_filter_level": 99.0,
+  "JointGenotyping.vqsr_indel_filter_level": 99.0,
   "JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"],
   "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"],
 

diff --git a/.../broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/shard_vcfs_high_memory.json b/.../broad/dna_seq/germline/joint_genotyping/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/...s/broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/shard_vcfs_low_memory.json b/...s/broad/dna_seq/germline/joint_genotyping/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",