Scale down GQ in CombineBatches

Author: mwalker174

wdl/CleanVcfChromosome.wdl

@@ -323,7 +323,6 @@ workflow CleanVcfChromosome {
     input:
       vcf=FinalCleanup.final_cleaned_shard,
       ploidy_table=ploidy_table,
-      args="--scale-down-gq",
       output_prefix="~{prefix}.final_format",
       script=svtk_to_gatk_script,
       sv_pipeline_docker=sv_pipeline_docker,

wdl/CombineBatches.wdl

@@ -112,7 +112,7 @@ workflow CombineBatches {
       input:
         vcf=reformatted_vcf,
         ploidy_table=CreatePloidyTableFromPed.out,
-        args="--fix-end --add-sr-pos",
+        args="--fix-end --add-sr-pos --scale-down-gq",
         output_prefix=basename(vcf, ".vcf.gz") + ".reformat_gatk",
         bothside_pass_list=CombineSRBothsidePass.out,
         background_fail_list=CombineBackgroundFail.outfile,