Added depth params to makegq/svconcordancepbsample

broadinstitute · Feb 22, 2025 · 2988256 · 2988256
1 parent a2f8587
commit 2988256
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Showing 2 changed files with 19 additions and 1 deletion.
diff --git a/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl b/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl
@@ -45,6 +45,10 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
     Float? pesr_size_similarity_strict = 0.5
     Int? pesr_breakend_window_strict = 5000
 
+    Float? depth_interval_overlap_strict = 0.5
+    Float? depth_size_similarity_strict = 0.0
+    Int? depth_breakend_window_strict = 10000000
+
     File? clustering_config_strict
     File? stratification_config_strict
     Array[String]? track_names_strict
@@ -54,6 +58,10 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
     Float? pesr_size_similarity_loose = 0
     Int? pesr_breakend_window_loose = 5000
 
+    Float? depth_interval_overlap_loose = 0.3
+    Float? depth_size_similarity_loose = 0.0
+    Int? depth_breakend_window_loose = 10000000
+
     File? clustering_config_loose
     File? stratification_config_loose
     Array[String]? track_names_loose
@@ -197,6 +205,9 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
         pesr_interval_overlap=pesr_interval_overlap_loose,
         pesr_size_similarity=pesr_size_similarity_loose,
         pesr_breakend_window=pesr_breakend_window_loose,
+        depth_interval_overlap=depth_interval_overlap_loose,
+        depth_size_similarity=depth_size_similarity_loose,
+        depth_breakend_window=depth_breakend_window_loose,
         clustering_config = clustering_config_loose,
         stratification_config = stratification_config_loose,
         track_names = track_names_loose,
@@ -219,6 +230,9 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
         pesr_interval_overlap=pesr_interval_overlap_strict,
         pesr_size_similarity=pesr_size_similarity_strict,
         pesr_breakend_window=pesr_breakend_window_strict,
+        depth_interval_overlap=depth_interval_overlap_strict,
+        depth_size_similarity=depth_size_similarity_strict,
+        depth_breakend_window=depth_breakend_window_strict,
         clustering_config = clustering_config_strict,
         stratification_config = stratification_config_strict,
         track_names = track_names_strict,

diff --git a/wdl/SVConcordancePacBioSample.wdl b/wdl/SVConcordancePacBioSample.wdl
@@ -20,6 +20,10 @@ workflow SVConcordancePacBioSample {
     Float? pesr_size_similarity
     Int? pesr_breakend_window
 
+    Float? depth_interval_overlap
+    Float? depth_size_similarity
+    Int? depth_breakend_window
+
     File? clustering_config
     File? stratification_config
     Array[String]? track_names
@@ -61,7 +65,7 @@ workflow SVConcordancePacBioSample {
         truth_vcf=PrepPacBioVcf.out,
         eval_vcf=sample_vcf,
         output_prefix="~{prefix}.concordance.~{tool_names[i]}.~{sample_id}.unsorted",
-        additional_args="--pesr-interval-overlap ~{pesr_interval_overlap} --pesr-size-similarity ~{pesr_size_similarity} --pesr-breakend-window ~{pesr_breakend_window}",
+        additional_args="--pesr-interval-overlap ~{pesr_interval_overlap} --pesr-size-similarity ~{pesr_size_similarity} --pesr-breakend-window ~{pesr_breakend_window} --depth-interval-overlap ~{depth_interval_overlap} --depth-size-similarity ~{depth_size_similarity} --depth-breakend-window ~{depth_breakend_window}",
         clustering_config=clustering_config,
         stratification_config=stratification_config,
         track_names=track_names,