diff --git a/HISTORY.rst b/HISTORY.rst index c5394abda..bc2f8fffc 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -20,6 +20,9 @@ End-User Summary - Small extension of "Resolution proposal" template (#472). - Adjusting wrong release name to "anthenea" (#479). - Adding "show all variant carriers" feature (#470). +- Properly display the clinvar annotations that we have in the database (#464). +- Adjusting default frequency filters for "clinvar pathogenic" filter: remove all threshold (#464). +- Adding note about difference with upstream Clinvar (#464). Full Change List ================ @@ -35,6 +38,9 @@ Full Change List - Small extension of "Resolution proposal" template (#472). - Adjusting wrong release name to "anthenea" (#479). - Adding "show all variant carriers" feature (#470). +- Properly display the clinvar annotations that we have in the database (#464). +- Adjusting default frequency filters for "clinvar pathogenic" filter: remove all threshold (#464). +- Adding note about difference with upstream Clinvar (#464). ------ v1.2.0 diff --git a/varfish/static/js/filter_form.js b/varfish/static/js/filter_form.js index 4075a7653..e366e63f8 100644 --- a/varfish/static/js/filter_form.js +++ b/varfish/static/js/filter_form.js @@ -1873,7 +1873,7 @@ function loadPresets(element) { $("#input-presets-flags").val("flags-default") } else if (presetsName == "clinvar") { $("#input-presets-inheritance").val("inheritance-mitochondrial") - $("#input-presets-frequency").val("frequency-recessive-relaxed") + $("#input-presets-frequency").val("frequency-all") $("#input-presets-impact").val("impact-any") $("#input-presets-quality").val("quality-strict") $("#input-presets-region").val("region-whole-genome") diff --git a/variants/query_presets.py b/variants/query_presets.py index 5c822b6d8..bb7d6e50f 100644 --- a/variants/query_presets.py +++ b/variants/query_presets.py @@ -1049,7 +1049,7 @@ class _QuickPresetList: #: Clinvar pathogenic presets clinvar_pathogenic: QuickPresets = QuickPresets( inheritance=Inheritance.AFFECTED_CARRIERS, - frequency=Frequency.RECESSIVE_RELAXED, + frequency=Frequency.ANY, impact=Impact.ANY, quality=Quality.STRICT, chromosomes=Chromosomes.WHOLE_GENOME, diff --git a/variants/templates/variants/filter_result/header.html b/variants/templates/variants/filter_result/header.html index 978935b04..f9822e61d 100644 --- a/variants/templates/variants/filter_result/header.html +++ b/variants/templates/variants/filter_result/header.html @@ -68,7 +68,7 @@