diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl b/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl
index 39bb552814..827d116c11 100644
--- a/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl
+++ b/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl
@@ -15,7 +15,7 @@ workflow AnnotationFiltration {
     File ref_dict
     File? funcotator_interval_list
 
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     File? custom_data_source_tar_gz
   }
 
diff --git a/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json b/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json
index d87a07c1ea..c8907ba8a2 100644
--- a/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json
+++ b/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json
@@ -10,6 +10,6 @@
   "AnnotationFiltration.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
   "AnnotationFiltration.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
 
-  "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0",
+  "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.6.1.0",
   "AnnotationFiltration.custom_data_source_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz"
 }
diff --git a/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json b/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json
index 6f36aeaafa..d4ab9d499b 100644
--- a/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json
+++ b/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json
@@ -8,6 +8,6 @@
   "AnnotationFiltration.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
   "AnnotationFiltration.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
 
-  "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0",
+  "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.6.1.0",
   "AnnotationFiltration.custom_data_source_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz"
 }
diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.wdl b/pipelines/broad/arrays/validate_chip/ValidateChip.wdl
index b6c03c19f0..ef664d5760 100644
--- a/pipelines/broad/arrays/validate_chip/ValidateChip.wdl
+++ b/pipelines/broad/arrays/validate_chip/ValidateChip.wdl
@@ -324,7 +324,7 @@ task GenotypeConcordance {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gatk/gatk:4.2.6.1"
+    docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     disks: "local-disk " + disk_size + " HDD"
     memory: "7000 MiB"
     preemptible: preemptible_tries
diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
index bf30156d98..d7786dd7dd 100644
--- a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
+++ b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
@@ -214,7 +214,7 @@ workflow JointGenotyping {
         extract_extra_args = extract_extra_args,
         resource_args = resource_args,
         output_prefix = callset_name,
-        gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     }
   } 
   if (!run_vets) {
diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl
index 06722fc971..a6ad2c417a 100644
--- a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl
+++ b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl
@@ -168,7 +168,7 @@ workflow UltimaGenomicsJointGenotyping {
       extract_extra_args = "--mode SNP",
       train_extra_args = "--mode SNP",
       score_extra_args = "--mode SNP",
-      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   call Filtering.JointVcfFiltering as TrainAndApplyFilteringModelINDELs {
@@ -184,7 +184,7 @@ workflow UltimaGenomicsJointGenotyping {
       extract_extra_args = "--mode INDEL",
       train_extra_args = "--mode INDEL",
       score_extra_args = "--mode INDEL",
-      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   call FilteringThreshold.ExtractOptimizeSingleSample as FindFilteringThresholdAndFilter {
diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
index 4012c2f35f..d244613fc1 100644
--- a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
+++ b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
@@ -26,8 +26,8 @@ workflow ReblockGVCF {
 
   String gvcf_basename = basename(gvcf, gvcf_file_extension)
   # docker images
-  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
-  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0"
+  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
+  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0"
   String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure
 
   # make sure either gcp or azr is supplied as cloud_provider input
diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
index 0162c6c617..23d92b2b45 100644
--- a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
+++ b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
@@ -68,8 +68,8 @@ workflow ExomeGermlineSingleSample {
   }
 
   # docker images
-  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
-  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0"
+  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
+  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0"
   String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure
 
   # make sure either gcp or azr is supplied as cloud_provider input
diff --git a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl
index 0e9fc75db1..995b2a0e63 100644
--- a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl
+++ b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl
@@ -40,8 +40,8 @@ workflow VariantCalling {
   }
 
   # docker images
-  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
-  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0"
+  String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
+  String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0"
   String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure
 
   String gatk_1_3_docker_gcp = "us.gcr.io/broad-gotc-prod/gatk:1.3.0-4.2.6.1-1649964384"
diff --git a/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl b/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl
index 80863f4d14..fa15704349 100644
--- a/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl
+++ b/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl
@@ -533,7 +533,7 @@ task gatk_baserecalibrator {
     }
 
     runtime {
-        docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         memory: mem + " MiB"
         disks: "local-disk " + disk_space + " HDD"
         preemptible: preemptible
@@ -580,7 +580,7 @@ task gatk_applybqsr {
     }
     
     runtime {
-        docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         memory: mem + " MiB"
         disks: "local-disk " + disk_space + " HDD"
         preemptible: preemptible
diff --git a/scripts/BuildAFComparisonTable.wdl b/scripts/BuildAFComparisonTable.wdl
index 1a0b3b81bb..44dac9bc3e 100644
--- a/scripts/BuildAFComparisonTable.wdl
+++ b/scripts/BuildAFComparisonTable.wdl
@@ -117,7 +117,7 @@ task AnnotateWithAF_t {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     disks: "local-disk " + disk_size + " HDD"
     memory: mem + " GB" # some of the gnomad vcfs are like 38 gigs so maybe need more ?
   }
@@ -145,7 +145,7 @@ task GatherVCFsCloud {
     >>>
 
     runtime {
-            docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+            docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
             disks: "local-disk " + disk_size + " HDD"
             memory: "16 GB"
         }
@@ -169,7 +169,7 @@ task MakeSitesOnlyVcf {
     >>>
 
     runtime {
-        docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         disks: "local-disk " + disk_size + " HDD"
         memory: "16 GB"
     }
@@ -224,7 +224,7 @@ task VariantsToTable {
     >>>
 
     runtime {
-        docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         disks: "local-disk " + disk_size + " HDD"
         memory: "16 GB"
     }
@@ -280,7 +280,7 @@ task RemoveSymbolicAlleles {
     File output_vcf_index = "~{output_basename}.vcf.gz.tbi"
   }
   runtime {
-    docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     disks: "local-disk " + disk_size + " HDD"
     memory: "4 GB"
   }
diff --git a/scripts/RemoveBadSitesByID.wdl b/scripts/RemoveBadSitesByID.wdl
index 378c26e31c..9299d7e96a 100644
--- a/scripts/RemoveBadSitesByID.wdl
+++ b/scripts/RemoveBadSitesByID.wdl
@@ -129,7 +129,7 @@ task SplitX {
     >>>
 
     runtime {
-        docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         disks: "local-disk " + disk_size + "  HDD"
         memory: "16 GB"
     }
@@ -215,7 +215,7 @@ task RemoveBadSitesFromVcf {
     >>>
 
     runtime {
-                docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+                docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         disks: "local-disk 100 HDD"
         memory: "16 GB"
     }
diff --git a/tasks/broad/BamProcessing.wdl b/tasks/broad/BamProcessing.wdl
index cf4ff4d4e2..32139f2eed 100644
--- a/tasks/broad/BamProcessing.wdl
+++ b/tasks/broad/BamProcessing.wdl
@@ -136,7 +136,7 @@ task BaseRecalibrator {
     File ref_fasta_index
     Int bqsr_scatter
     Int preemptible_tries
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   Float ref_size = size(ref_fasta, "GiB") + size(ref_fasta_index, "GiB") + size(ref_dict, "GiB")
@@ -188,7 +188,7 @@ task ApplyBQSR {
     Int compression_level
     Int bqsr_scatter
     Int preemptible_tries
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int memory_multiplier = 1
     Int additional_disk = 20
     Boolean bin_base_qualities = true
@@ -247,7 +247,7 @@ task GatherBqsrReports {
     Array[File] input_bqsr_reports
     String output_report_filename
     Int preemptible_tries
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command {
diff --git a/tasks/broad/CheckContaminationSomatic.wdl b/tasks/broad/CheckContaminationSomatic.wdl
index dd70628962..5cc8715e91 100644
--- a/tasks/broad/CheckContaminationSomatic.wdl
+++ b/tasks/broad/CheckContaminationSomatic.wdl
@@ -14,7 +14,7 @@ task CalculateSomaticContamination {
         File contamination_vcf_index
 
         # runtime
-        String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.2.4.1"
+        String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         File? gatk_override
         Int? additional_disk
         Int memory_mb = 3000
diff --git a/tasks/broad/DragenTasks.wdl b/tasks/broad/DragenTasks.wdl
index 57146b7a02..11aae23dbb 100644
--- a/tasks/broad/DragenTasks.wdl
+++ b/tasks/broad/DragenTasks.wdl
@@ -25,7 +25,7 @@ task CalibrateDragstrModel {
     File alignment ## can handle cram or bam.
     File alignment_index
     #Setting default docker value for workflows that haven't yet been azurized.
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int preemptible_tries = 3
     Int threads = 4
     Int? memory_mb
diff --git a/tasks/broad/GermlineVariantDiscovery.wdl b/tasks/broad/GermlineVariantDiscovery.wdl
index 13882cb6df..7538290e08 100644
--- a/tasks/broad/GermlineVariantDiscovery.wdl
+++ b/tasks/broad/GermlineVariantDiscovery.wdl
@@ -99,7 +99,7 @@ task HaplotypeCaller_GATK4_VCF {
     Boolean use_spanning_event_genotyping = true
     File? dragstr_model
     #Setting default docker value for workflows that haven't yet been azurized.
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int memory_multiplier = 1
   }
   
@@ -261,7 +261,7 @@ task HardFilterVcf {
     String vcf_basename
     File interval_list
     Int preemptible_tries
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   Int disk_size = ceil(2 * size(input_vcf, "GiB")) + 20
@@ -337,7 +337,7 @@ task CNNScoreVariants {
     File ref_fasta_index
     File ref_dict
     Int preemptible_tries
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   Int disk_size = ceil(size(bamout, "GiB") + size(ref_fasta, "GiB") + (size(input_vcf, "GiB") * 2))
@@ -394,7 +394,7 @@ task FilterVariantTranches {
     File dbsnp_resource_vcf_index
     String info_key
     Int preemptible_tries
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   Int disk_size = ceil(size(hapmap_resource_vcf, "GiB") +
diff --git a/tasks/broad/IlluminaGenotypingArrayTasks.wdl b/tasks/broad/IlluminaGenotypingArrayTasks.wdl
index 49971de93e..ab362104a9 100644
--- a/tasks/broad/IlluminaGenotypingArrayTasks.wdl
+++ b/tasks/broad/IlluminaGenotypingArrayTasks.wdl
@@ -404,7 +404,7 @@ task SelectVariants {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size + " HDD"
     memory: "3500 MiB"
@@ -441,7 +441,7 @@ task SelectIndels {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size + " HDD"
     memory: "3500 MiB"
@@ -577,7 +577,7 @@ task SubsetArrayVCF {
   }
 
   runtime {
-    docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size + " HDD"
     memory: "3500 MiB"
@@ -676,7 +676,7 @@ task ValidateVariants {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size + " HDD"
     memory: "3500 MiB"
diff --git a/tasks/broad/ImputationTasks.wdl b/tasks/broad/ImputationTasks.wdl
index 02bdb2e603..793ae119b2 100644
--- a/tasks/broad/ImputationTasks.wdl
+++ b/tasks/broad/ImputationTasks.wdl
@@ -65,7 +65,7 @@ task GenerateChunk {
     Int disk_size_gb = ceil(2*size(vcf, "GiB")) + 50 # not sure how big the disk size needs to be since we aren't downloading the entire VCF here
     Int cpu = 1
     Int memory_mb = 8000
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
   Int command_mem = memory_mb - 1000
   Int max_heap = memory_mb - 500
@@ -112,7 +112,7 @@ task CountVariantsInChunks {
     File panel_vcf
     File panel_vcf_index
 
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 4000
     Int disk_size_gb = 2 * ceil(size([vcf, vcf_index, panel_vcf, panel_vcf_index], "GiB")) + 20
@@ -266,7 +266,7 @@ task GatherVcfs {
     Array[File] input_vcfs
     String output_vcf_basename
 
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 16000
     Int disk_size_gb = ceil(3*size(input_vcfs, "GiB"))
@@ -336,7 +336,7 @@ task UpdateHeader {
     String basename
 
     Int disk_size_gb = ceil(4*(size(vcf, "GiB") + size(vcf_index, "GiB"))) + 20
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 8000
   }
@@ -372,7 +372,7 @@ task RemoveSymbolicAlleles {
     String output_basename
 
     Int disk_size_gb = ceil(3*(size(original_vcf, "GiB") + size(original_vcf_index, "GiB")))
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 4000
   }
@@ -659,7 +659,7 @@ task SubsetVcfToRegion {
     Int disk_size_gb = ceil(2*size(vcf, "GiB")) + 50 # not sure how big the disk size needs to be since we aren't downloading the entire VCF here
     Int cpu = 1
     Int memory_mb = 8000
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
   Int command_mem = memory_mb - 1000
   Int max_heap = memory_mb - 500
@@ -754,7 +754,7 @@ task SelectVariantsByIds {
     File ids
     String basename
 
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 16000
     Int disk_size_gb = ceil(1.2*size(vcf, "GiB")) + 100
@@ -820,7 +820,7 @@ task InterleaveVariants {
     Array[File] vcfs
     String basename
 
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 16000
     Int disk_size_gb = ceil(3.2*size(vcfs, "GiB")) + 100
diff --git a/tasks/broad/JointGenotypingTasks.wdl b/tasks/broad/JointGenotypingTasks.wdl
index a38fdfc614..9e6378a9b5 100644
--- a/tasks/broad/JointGenotypingTasks.wdl
+++ b/tasks/broad/JointGenotypingTasks.wdl
@@ -51,7 +51,7 @@ task SplitIntervalList {
     Int machine_mem_mb = 3750
     String scatter_mode = "BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW"
     String? extra_args
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   parameter_meta {
@@ -94,7 +94,7 @@ task ImportGVCFs {
     Int machine_mem_mb = 30000
     Int batch_size
 
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command <<<
@@ -159,7 +159,7 @@ task GenotypeGVCFs {
     Int machine_mem_mb = 26000
     # This is needed for gVCFs generated with GATK3 HaplotypeCaller
     Boolean allow_old_rms_mapping_quality_annotation_data = false
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   parameter_meta {
@@ -216,7 +216,7 @@ task GnarlyGenotyper {
     String dbsnp_vcf
     Boolean make_annotation_db = false
 
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int machine_mem_mb = 26000
     Int disk_size_gb = ceil(size(workspace_tar, "GiB") + size(ref_fasta, "GiB") + size(dbsnp_vcf, "GiB") * 3)
   }
@@ -277,7 +277,7 @@ task HardFilterAndMakeSitesOnlyVcf {
 
     Int disk_size_gb
     Int machine_mem_mb = 3750
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command <<<
@@ -339,7 +339,7 @@ task IndelsVariantRecalibrator {
 
     Int disk_size_gb
     Int machine_mem_mb = 26000
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command <<<
@@ -404,7 +404,7 @@ task SNPsVariantRecalibratorCreateModel {
 
     Int disk_size_gb
     Int machine_mem_mb = 104000
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command <<<
@@ -468,7 +468,7 @@ task SNPsVariantRecalibrator {
     Int max_gaussians = 6
 
     Int disk_size_gb
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int? machine_mem_mb
 
   }
@@ -533,7 +533,7 @@ task GatherTranches {
     String mode
     Int disk_size_gb
     Int machine_mem_mb = 7500
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   parameter_meta {
@@ -607,7 +607,7 @@ task ApplyRecalibration {
     Boolean use_allele_specific_annotations
     Int disk_size_gb
     Int machine_mem_mb = 7000
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command <<<
@@ -658,7 +658,7 @@ task GatherVcfs {
     String output_vcf_name
     Int disk_size_gb
     Int machine_mem_mb = 7000
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   parameter_meta {
@@ -706,7 +706,7 @@ task SelectFingerprintSiteVariants {
     String base_output_name
     Int disk_size_gb
     Int machine_mem_mb = 7500
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   parameter_meta {
@@ -759,7 +759,7 @@ task CollectVariantCallingMetrics {
     File ref_dict
     Int disk_size_gb
     Int machine_mem_mb = 7500
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command <<<
@@ -798,7 +798,7 @@ task GatherVariantCallingMetrics {
     String output_prefix
     Int disk_size_gb
     Int machine_mem_mb = 3000
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   parameter_meta {
@@ -879,7 +879,7 @@ task CrossCheckFingerprint {
     String output_base_name
     Boolean scattered = false
     Array[String] expected_inconclusive_samples = []
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int? machine_mem_mb
     Int disk = 100
   }
@@ -1000,7 +1000,7 @@ task GetFingerprintingIntervalIndices {
   input {
     Array[File] unpadded_intervals
     File haplotype_database
-    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb = 10
     Int machine_mem_mb = 3750
   }
@@ -1114,7 +1114,7 @@ task CalculateAverageAnnotations {
     File vcf
     Array[String] annotations_to_divide = ["ASSEMBLED_HAPS", "FILTERED_HAPS", "TREE_SCORE"]
 
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb = ceil(size(vcf, "GB") + 50)
     Int memory_mb = 12000
     Int preemptible = 3
diff --git a/tasks/broad/Qc.wdl b/tasks/broad/Qc.wdl
index ff0d1b3fcf..def53ab0df 100644
--- a/tasks/broad/Qc.wdl
+++ b/tasks/broad/Qc.wdl
@@ -623,7 +623,7 @@ task ValidateVCF {
     Boolean is_gvcf = true
     String? extra_args
     #Setting default docker value for workflows that haven't yet been azurized.
-    String docker_path = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker_path = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int machine_mem_mb = 7000
   }
 
diff --git a/tasks/broad/RNAWithUMIsTasks.wdl b/tasks/broad/RNAWithUMIsTasks.wdl
index 32cef74b85..7997da9274 100644
--- a/tasks/broad/RNAWithUMIsTasks.wdl
+++ b/tasks/broad/RNAWithUMIsTasks.wdl
@@ -278,7 +278,7 @@ task GetSampleName {
   input {
     File bam
 
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 1000
     Int disk_size_gb = ceil(2.0 * size(bam, "GiB")) + 10
@@ -852,7 +852,7 @@ task CalculateContamination {
     File population_vcf
     File population_vcf_index
     # runtime
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int cpu = 1
     Int memory_mb = 8192
     Int disk_size_gb = 256
@@ -965,7 +965,7 @@ task TransferReadTags {
     File aligned_bam
     File ubam
     String output_basename
-    String docker = "us.gcr.io/broad-gatk/gatk:4.4.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int memory_mb = 16000
     Int disk_size_gb = ceil(2 * size(aligned_bam, "GiB")) + ceil(2 * size(ubam, "GiB")) + 128
   }
@@ -994,7 +994,7 @@ task PostprocessTranscriptomeForRSEM {
     String prefix
     File input_bam # the input must be queryname sorted
     Int disk_size_gb = ceil(3*size(input_bam,"GiB")) + 128
-    String docker = "us.gcr.io/broad-gatk/gatk:4.2.6.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int memory_mb = 16000
   }
 
@@ -1019,7 +1019,7 @@ task PostprocessTranscriptomeForRSEM {
 task CreateEmptyFile {
   input {
     Int disk_size_gb = 128
-    String docker = "us.gcr.io/broad-gatk/gatk:4.2.6.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int memory_mb = 4096
   }
 
diff --git a/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl b/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl
index 98af0810f5..431362da87 100644
--- a/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl
+++ b/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl
@@ -326,7 +326,7 @@ task HardThresholdVCF {
     String output_basename
     String score_key
     Int disk_size
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
   }
 
   command <<<
@@ -384,7 +384,7 @@ task AnnotateSampleVCF {
         File input_vcf_index
         String output_basename
         Int disk_size = ceil(size(input_vcf, "GB") * 2) + 50
-        String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
         File ref_fasta
         File ref_fasta_index
         File ref_dict
diff --git a/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl b/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl
index 19831dbaa2..739b44202c 100644
--- a/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl
+++ b/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl
@@ -56,7 +56,7 @@ task SplitCram {
     String base_file_name
     Int reads_per_file
 
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb = ceil(3 * size(input_cram_bam, "GiB") + 20)
     Int cpu = 1
     Int memory_gb = 10
@@ -269,7 +269,7 @@ task MarkDuplicatesSpark {
     Array[File] input_bams
     String output_bam_basename
     Boolean save_bam_file
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb
     Int cpu = 32
     Int memory_mb = if 4 * ceil(size(input_bams, "MB")) / 4000 > 600000 then 300000 else 208000
@@ -319,7 +319,7 @@ task ExtractSampleNameFlowOrder{
     File input_bam
     References references
     
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb = ceil(size(input_bam, "GB") + size(references.ref_fasta, "GB") + 20)
     Int cpu = 1
     Int memory_mb = 2000
@@ -480,7 +480,7 @@ task HaplotypeCaller {
     Boolean native_sw = false
     String? contamination_extra_args 
     
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb = ceil((size(input_bam_list, "GB")) + size(references.ref_fasta, "GB") + size(references.ref_fasta_index, "GB") + size(references.ref_dict, "GB") + 60)
     Int cpu = 2
     Int memory_mb = 12000
@@ -591,7 +591,7 @@ task ConvertGVCFtoVCF {
     String output_vcf_name
     References references
 
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb = ceil(2 * size(input_gvcf, "GB") + size(references.ref_fasta, "GB") + size(input_gvcf_index, "GB") + 20)
     Int cpu = 1
     Int memory_mb = 12000
@@ -947,7 +947,7 @@ task AnnotateVCF {
     String flow_order
     String final_vcf_base_name
 
-    String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+    String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
     Int disk_size_gb = ceil(2 * size(input_vcf, "GB") + size(references.ref_fasta, "GB") + size(reference_dbsnp, "GB") + 20)
     Int cpu = 1
     Int memory_mb = 15000
diff --git a/verification/VerifyNA12878.wdl b/verification/VerifyNA12878.wdl
index b7ecfe1dbe..3d5720df4d 100644
--- a/verification/VerifyNA12878.wdl
+++ b/verification/VerifyNA12878.wdl
@@ -86,7 +86,7 @@ task RunValidation {
     }
 
     runtime {
-        docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
+        docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
 
         memory: machine_mem + " MiB"
         disks: "local-disk " + select_first([disk_space, 100]) + if use_ssd then " SSD" else " HDD"
diff --git a/verification/VerifyUltimaGenomicsJointGenotyping.wdl b/verification/VerifyUltimaGenomicsJointGenotyping.wdl
index aa0c6ded02..f85d5bfe3d 100644
--- a/verification/VerifyUltimaGenomicsJointGenotyping.wdl
+++ b/verification/VerifyUltimaGenomicsJointGenotyping.wdl
@@ -31,6 +31,15 @@ workflow VerifyJointGenotyping {
         test_gvcf = test_vcfs[idx],
         truth_gvcf = truth_vcfs[idx]
     }
+
+    call VerifyTasks.CompareVCFsVerbosely as CompareFilteredVcfsVerbosely {
+      input:
+        test_vcf = test_vcfs[idx],
+        truth_vcf = truth_vcfs[idx],
+        extra_args = " --ignore-attribute AVERAGE_TREE_SCORE --ignore-attribute CALIBRATION_SENSITIVITY "
+      + "--ignore-attribute TREE_SCORE --ignore-attribute SCORE --ignore-filters --ignore-attribute AS_FilterStatus "
+      + "--ignore-attribute ExcessHet --ignore-star-attributes --allow-nan-mismatch --ignore-attribute END"
+    }
   }
 
   call MetricsVerification.VerifyMetrics {
diff --git a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl
index 28a7924209..a735a2330e 100755
--- a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl
+++ b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl
@@ -109,6 +109,15 @@ workflow VerifyUltimaGenomicsWholeGenomeGermline {
       patternForLinesToExcludeFromComparison = "^##"
   }
 
+  call Tasks.CompareVCFsVerbosely as CompareGVcfsVerbosely {
+    input:
+      test_vcf = test_gvcf,
+      truth_vcf = truth_gvcf,
+      extra_args = " --ignore-attribute AVERAGE_TREE_SCORE --ignore-attribute CALIBRATION_SENSITIVITY "
+    + "--ignore-attribute TREE_SCORE --ignore-attribute SCORE --ignore-filters --ignore-attribute AS_FilterStatus "
+    + "--ignore-attribute ExcessHet --ignore-star-attributes --allow-nan-mismatch --ignore-attribute END"
+  }
+
   call VerifyNA12878.VerifyNA12878 {
     input:
       vcf_files = [test_filtered_vcf, truth_filtered_vcf],