From e14de3e3383b68b3707cdef69fcaafd46e50cfe0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 18 Mar 2024 13:24:25 -0400 Subject: [PATCH] add better filtration for reloading SNV/INDEL variants --- seqr/views/utils/variant_utils.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/seqr/views/utils/variant_utils.py b/seqr/views/utils/variant_utils.py index 3daba835ca..4af1fb3450 100644 --- a/seqr/views/utils/variant_utils.py +++ b/seqr/views/utils/variant_utils.py @@ -102,10 +102,13 @@ def update_project_saved_variant_json(project_id, family_guids=None, dataset_typ def saved_variants_dataset_type_filter(dataset_type): xpos_filter_key = 'xpos__gte' if dataset_type == Sample.DATASET_TYPE_MITO_CALLS else 'xpos__lt' - return { - 'alt__isnull': dataset_type == Sample.DATASET_TYPE_SV_CALLS, - xpos_filter_key: get_xpos('M', 1), - } + dataset_filter = {xpos_filter_key: get_xpos('M', 1)} + if dataset_type == Sample.DATASET_TYPE_SV_CALLS: + dataset_filter['alt__isnull'] = True + else: + # Filter out manual variants with invalid characters, such as those used for STRs + dataset_filter['alt__regex'] = '^[ACGT]$' + return dataset_filter def parse_saved_variant_json(variant_json, family):