Add --max-mnp-distance input argument to vc-gatk4-hc

genialis · Dec 16, 2024 · 18015ca · 18015ca
1 parent 1aac953
commit 18015ca
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diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -17,6 +17,7 @@ Added
 - Use generic permission filters when filtering variants by related models
 - Return only distinct ``VariantExperiment`` objects
 - Add ``--bam-output`` input argument to ``vc-gatk4-hc``
+- Add ``--max-mnp-distance`` input argument to ``vc-gatk4-hc``
 
 
 ===================

diff --git a/resolwe_bio/processes/variant_calling/gatk4_hc.py b/resolwe_bio/processes/variant_calling/gatk4_hc.py
@@ -134,6 +134,12 @@ class Advanced:
                 ],
                 disabled="!bam_out",
             )
+            max_mnp_distance = IntegerField(
+                label="Max MNP distance",
+                default=0,
+                description="Two or more phased substitutions separated by this distance or less are merged into MNPs. "
+                "Set 0 to disable.",
+            )
 
         advanced = GroupField(Advanced, label="Advanced options")
 
@@ -180,6 +186,8 @@ def run(self, inputs, outputs):
             inputs.stand_call_conf,
             "--tmp-dir",
             TMPDIR,
+            "--max-mnp-distance",
+            inputs.advanced.max_mnp_distance,
         ]
 
         if inputs.advanced.soft_clipped: