Set allow_overlaps=true, naive=false in ConcatCpxCnvVcfs (#384)

broadinstitute · Aug 8, 2022 · 9e32e40 · 9e32e40
1 parent bd9a7ae
commit 9e32e40
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/wdl/ScatterCpxGenotyping.wdl b/wdl/ScatterCpxGenotyping.wdl
@@ -118,7 +118,7 @@ workflow ScatterCpxGenotyping {
       input:
         vcfs=GenotypeShard.cpx_depth_gt_resolved_vcf,
         vcfs_idx=GenotypeShard.cpx_depth_gt_resolved_vcf_idx,
-        naive=true,
+        allow_overlaps=true,
         outfile_prefix="~{prefix}.regenotyped",
         sv_base_mini_docker=sv_base_mini_docker,
         runtime_attr_override=runtime_override_concat_cpx_cnv_vcfs