diff --git a/definitions/tools/bcftools_merge.cwl b/definitions/tools/bcftools_merge.cwl
index 2c5de672..4c45df4b 100644
--- a/definitions/tools/bcftools_merge.cwl
+++ b/definitions/tools/bcftools_merge.cwl
@@ -9,7 +9,7 @@ requirements:
     - class: ResourceRequirement
       ramMin: 4000
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.9"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
 
 inputs:
     force_merge:
diff --git a/definitions/tools/filter_known_variants.cwl b/definitions/tools/filter_known_variants.cwl
index 85e2a3b5..fa42a8c7 100644
--- a/definitions/tools/filter_known_variants.cwl
+++ b/definitions/tools/filter_known_variants.cwl
@@ -6,7 +6,7 @@ label: "Adds an INFO tag (VALIDATED) flagging variants in the pipeline vcf prese
 
 requirements:
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.9"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
     - class: ResourceRequirement
       ramMin: 8000
     - class: InitialWorkDirRequirement
diff --git a/definitions/tools/filter_sv_vcf_depth.cwl b/definitions/tools/filter_sv_vcf_depth.cwl
index 94ffb610..939bfce7 100644
--- a/definitions/tools/filter_sv_vcf_depth.cwl
+++ b/definitions/tools/filter_sv_vcf_depth.cwl
@@ -8,7 +8,7 @@ requirements:
     - class: ResourceRequirement
       ramMin: 4000
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.9"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
     - class: InitialWorkDirRequirement
       listing:
       - entryname: "filter_sv_vcf_depth.sh"
diff --git a/definitions/tools/filter_sv_vcf_read_support.cwl b/definitions/tools/filter_sv_vcf_read_support.cwl
index 0ce89d98..915d1e3c 100644
--- a/definitions/tools/filter_sv_vcf_read_support.cwl
+++ b/definitions/tools/filter_sv_vcf_read_support.cwl
@@ -8,7 +8,7 @@ requirements:
     - class: ResourceRequirement
       ramMin: 4000
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.9"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
     - class: InitialWorkDirRequirement
       listing:
       - entryname: "filter_sv_vcf_read_support.sh"
diff --git a/definitions/tools/filter_sv_vcf_size.cwl b/definitions/tools/filter_sv_vcf_size.cwl
index 72422750..0b5dce25 100644
--- a/definitions/tools/filter_sv_vcf_size.cwl
+++ b/definitions/tools/filter_sv_vcf_size.cwl
@@ -8,7 +8,7 @@ requirements:
     - class: ResourceRequirement
       ramMin: 4000
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.9"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
     - class: InitialWorkDirRequirement
       listing:
       - entryname: "filter_sv_vcf_size.sh"
diff --git a/definitions/tools/intersect_known_variants.cwl b/definitions/tools/intersect_known_variants.cwl
index 8717432c..5b74fe1e 100644
--- a/definitions/tools/intersect_known_variants.cwl
+++ b/definitions/tools/intersect_known_variants.cwl
@@ -6,7 +6,7 @@ label: "Intersect passing validated variants and passing pipeline variants for u
 
 requirements:
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.9"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
     - class: ResourceRequirement
       ramMin: 8000
     - class: InitialWorkDirRequirement
diff --git a/definitions/tools/merge_vcf.cwl b/definitions/tools/merge_vcf.cwl
index 6efb3582..59b6d176 100644
--- a/definitions/tools/merge_vcf.cwl
+++ b/definitions/tools/merge_vcf.cwl
@@ -6,7 +6,7 @@ label: "vcf merge"
 baseCommand: ["/opt/bcftools/bin/bcftools", "concat"]
 requirements:
     - class: DockerRequirement
-      dockerPull: mgibio/bcftools-cwl:1.3.1
+      dockerPull: mgibio/bcftools-cwl:1.12
     - class: ResourceRequirement
       ramMin: 4000
 arguments:
diff --git a/definitions/tools/remove_end_tags.cwl b/definitions/tools/remove_end_tags.cwl
index c144a556..ac7bfb66 100644
--- a/definitions/tools/remove_end_tags.cwl
+++ b/definitions/tools/remove_end_tags.cwl
@@ -13,7 +13,7 @@ requirements:
     - class: ResourceRequirement
       ramMin: 4000
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.3.1"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
 inputs:
     vcf:
         type: File
diff --git a/definitions/tools/replace_vcf_sample_name.cwl b/definitions/tools/replace_vcf_sample_name.cwl
index ea730a15..6c1e82fa 100644
--- a/definitions/tools/replace_vcf_sample_name.cwl
+++ b/definitions/tools/replace_vcf_sample_name.cwl
@@ -9,7 +9,7 @@ requirements:
     - class: ResourceRequirement
       ramMin: 8000
     - class: DockerRequirement
-      dockerPull: "mgibio/bcftools-cwl:1.9"
+      dockerPull: "mgibio/bcftools-cwl:1.12"
     - class: InitialWorkDirRequirement
       listing:
       - entryname: "rename_sample.sh"