[TSPS-770] Update Beagle jar to remove trailing zeros from AF and DR2 annotations (#1747)

Author: salonishah11

pipeline_versions.txt

@@ -6,7 +6,7 @@ ExomeGermlineSingleSample	 3.2.7	2026-01-21
 ExomeReprocessing	 3.3.7	2026-01-21 
 IlluminaGenotypingArray	 1.12.27	2026-01-21 
 Imputation	 1.1.23	2025-10-03 
-ImputationBeagle	 2.4.2	2025-12-23 
+ImputationBeagle	 2.5.0	2026-01-27 
 JointGenotyping	 1.7.3	2025-08-11 
 MultiSampleSmartSeq2SingleNucleus	 2.2.4	2026-01-21 
 Multiome	 6.1.4	2026-01-22 

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.changelog.md

@@ -1,3 +1,8 @@
+# 2.5.0
+2026-01-27 (Date of Last Commit)
+
+* Updates Phase and Impute tasks docker image to remove trailing zeros from AF and DR2 annotations in the output VCF.
+
 # 2.4.2
 2025-12-23 (Date of Last Commit)
 

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.wdl

@@ -5,7 +5,7 @@ import "../../../../tasks/wdl/ImputationTasks.wdl" as tasks
 import "../../../../tasks/wdl/ImputationBeagleTasks.wdl" as beagleTasks
 
 workflow ImputationBeagle {
-  String pipeline_version = "2.4.2"
+  String pipeline_version = "2.5.0"
   String input_qc_version = "1.2.5"
   String quota_consumed_version = "1.1.0"
 

tasks/wdl/ImputationBeagleTasks.wdl

@@ -307,7 +307,7 @@ task Phase {
     Int start
     Int end
 
-    String beagle_docker = "us.gcr.io/broad-gotc-prod/imputation-beagle:2.0.0-d820c4e-1763720636"
+    String beagle_docker = "us.gcr.io/broad-gotc-prod/imputation-beagle:3.1.0-0b17ad0-1768971822"
     Int cpu = 8                    # This parameter is used as the nthreads input to Beagle which is part of how we make it determinstic.  Changing this value may change the output generated by the tool
     Int memory_mb = 32000          # value depends on chunk size, the number of samples in ref and target panel
     Int disk_size_gb = ceil((3 * size(dataset_vcf, "GiB")) + size(ref_panel_bref3, "GiB")) + 10
@@ -319,7 +319,7 @@ task Phase {
     set -e -o pipefail
 
     java -ea -XX:MaxRAMPercentage=90.0 -XX:MinRAMPercentage=90.0 -XX:-UseCompressedOops \
-    -jar /usr/gitc/beagle.d820c4e.jar \
+    -jar /usr/gitc/beagle.0b17ad0.jar \
     gt=~{dataset_vcf} \
     ref=~{ref_panel_bref3} \
     map=~{genetic_map_file} \
@@ -356,7 +356,7 @@ task Impute {
     Int end
     Boolean impute_with_allele_probabilities
 
-    String beagle_docker = "us.gcr.io/broad-gotc-prod/imputation-beagle:2.0.0-d820c4e-1763720636"
+    String beagle_docker = "us.gcr.io/broad-gotc-prod/imputation-beagle:3.1.0-0b17ad0-1768971822"
     Int cpu = 8                    # This parameter is used as the nthreads input to Beagle which is part of how we make it determinstic.  Changing this value may change the output generated by the tool
     Int memory_mb = 32000          # value depends on chunk size, the number of samples in ref and target panel
     Int disk_size_gb = ceil((3 * size(dataset_vcf, "GiB")) + size(ref_panel_bref3, "GiB")) + 10
@@ -366,7 +366,7 @@ task Impute {
     set -e -o pipefail
 
     java -ea -XX:MaxRAMPercentage=90.0 -XX:MinRAMPercentage=90.0 -XX:-UseCompressedOops \
-    -jar /usr/gitc/beagle.d820c4e.jar \
+    -jar /usr/gitc/beagle.0b17ad0.jar \
     gt=~{dataset_vcf} \
     ref=~{ref_panel_bref3} \
     map=~{genetic_map_file} \