Switch to GATK's --variant-output-filtering

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java

@@ -717,7 +717,9 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
                         toolParams.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
                     });
                 }
-                toolParams.add("--only-output-calls-starting-in-intervals");
+
+                toolParams.add("--variant-output-filtering");
+                toolParams.add("STARTS_IN");
             }
 
             if (ctx.getParams().optBoolean("variantCalling.GenotypeGVCFs.disableFileLocking", false))

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java

@@ -342,7 +342,8 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
                         extraArgs.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
                     });
 
-                    extraArgs.add("--ignore-variants-starting-outside-interval");
+                    extraArgs.add("--variant-output-filtering");
+                    extraArgs.add("STARTS_IN");
                 }
 
                 SelectVariantsWrapper wrapper = new SelectVariantsWrapper(job.getLogger());