TSPS-845 Optimizations to low pass imputation pipeline (#1800)

* split bcftools call task into 3 functions

* update glimpse phase task to not localize input vcf

* use ssds for tasks that localize large files and are preemptible

---------

Co-authored-by: Jose Soto <jsoto@broadinstitute.org>
Co-authored-by: GitHub Action <action@github.com>

Author: 3 people

pipeline_versions.txt

@@ -4,7 +4,7 @@ BuildIndices	 5.1.0	2026-02-13
 CramToUnmappedBams	 1.1.3	2024-08-02 
 ExomeGermlineSingleSample	 3.2.7	2026-01-21 
 ExomeReprocessing	 3.3.7	2026-01-21 
-Glimpse2LowPassImputation	 0.0.1	2026-02-26 
+Glimpse2LowPassImputation	 0.0.2	2026-03-19 
 IlluminaGenotypingArray	 1.12.27	2026-01-21 
 Imputation	 1.1.23	2025-10-03 
 ImputationBeagle	 3.0.1	2026-02-23 

pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.changelog.md

@@ -1,3 +1,8 @@
+# 0.0.2
+2026-03-19 (Date of Last Commit)
+
+* Optimizations to pipeline to run faster and more cheaply using the aou + anvil reference panel
+
 # 0.0.1
 2026-02-26 (Date of Last Commit)