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Prioritized variants - add QS filter #5640

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eec19af
add qs cutoff for prioritized search
hanars Oct 29, 2026
43f4859
update tests
hanars Oct 29, 2026
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18 changes: 9 additions & 9 deletions clickhouse_search/all_search_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,12 +305,12 @@ def test_standard_searches(self):
], project_families=SINGLE_FAMILY_PROJECT_FAMILIES, **VariantSearch.objects.get(name='De Novo/Dominant Permissive').search,
)

self._assert_expected_search([VARIANT2, MITO_VARIANT3], cached_variant_fields=[
{'selectedTranscript': CACHED_CONSEQUENCES_BY_KEY[2][0]}, {},
self._assert_expected_search([VARIANT2, GCNV_VARIANT3, MITO_VARIANT3], cached_variant_fields=[
{'selectedTranscript': CACHED_CONSEQUENCES_BY_KEY[2][0]}, {}, {},
], project_families=SINGLE_FAMILY_PROJECT_FAMILIES, **VariantSearch.objects.get(name='Recessive Restrictive').search)

self._assert_expected_search([VARIANT2, MITO_VARIANT3], cached_variant_fields=[
{'selectedTranscript': CACHED_CONSEQUENCES_BY_KEY[2][0]}, {},
self._assert_expected_search([VARIANT2, GCNV_VARIANT3, MITO_VARIANT3], cached_variant_fields=[
{'selectedTranscript': CACHED_CONSEQUENCES_BY_KEY[2][0]}, {}, {},
], project_families=SINGLE_FAMILY_PROJECT_FAMILIES, **VariantSearch.objects.get(name='Recessive Permissive').search)

def test_single_project_search(self):
Expand Down Expand Up @@ -451,8 +451,8 @@ def test_both_sample_types_search(self):
)

self._assert_expected_search(
[VARIANT2_BOTH_SAMPLE_TYPES, VARIANT3_BOTH_SAMPLE_TYPES, GCNV_VARIANT1, GCNV_VARIANT2, GCNV_VARIANT4],
inheritance_mode='any_affected', quality_filter={'min_gq': 40, 'min_qs': 20}, project_families=SINGLE_FAMILY_PROJECT_FAMILIES,
[VARIANT2_BOTH_SAMPLE_TYPES, VARIANT3_BOTH_SAMPLE_TYPES, GCNV_VARIANT1, GCNV_VARIANT3, GCNV_VARIANT4],
inheritance_mode='any_affected', quality_filter={'min_gq': 40, 'min_qs': 30}, project_families=SINGLE_FAMILY_PROJECT_FAMILIES,
)

self._assert_expected_search(
Expand Down Expand Up @@ -736,9 +736,9 @@ def test_quality_filter(self):
[SV_VARIANT4], quality_filter=quality_filter, project_families=SV_PROJECT_FAMILIES,
)

gcnv_quality_filter = {'min_gq': 40, 'min_qs': 20, 'min_hl': 5}
gcnv_quality_filter = {'min_gq': 40, 'min_qs': 30, 'min_hl': 5}
self._assert_expected_search(
[VARIANT2, MULTI_FAMILY_VARIANT, GCNV_VARIANT1, GCNV_VARIANT2, GCNV_VARIANT4, MITO_VARIANT1, MITO_VARIANT3], quality_filter=gcnv_quality_filter,
[VARIANT2, MULTI_FAMILY_VARIANT, GCNV_VARIANT1, GCNV_VARIANT3, GCNV_VARIANT4, MITO_VARIANT1, MITO_VARIANT3], quality_filter=gcnv_quality_filter,
)

sv_quality_filter = {'min_gq_sv': 40}
Expand All @@ -747,7 +747,7 @@ def test_quality_filter(self):
)

self._assert_expected_search(
[VARIANT2, MULTI_FAMILY_VARIANT, GCNV_VARIANT1, MITO_VARIANT1, MITO_VARIANT2], quality_filter={'min_gq': 40, 'min_qs': 30, 'vcf_filter': 'pass'},
[VARIANT2, MULTI_FAMILY_VARIANT, GCNV_VARIANT4, MITO_VARIANT1, MITO_VARIANT2], quality_filter={'min_gq': 40, 'min_qs': 200, 'vcf_filter': 'pass'},
)

self._assert_expected_search(
Expand Down
12 changes: 6 additions & 6 deletions clickhouse_search/fixtures/clickhouse_search.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1609,8 +1609,8 @@
"filters": [],
"sign": 1,
"calls": [
["HG00731", 2, 4, 13, true, 38717327, 38719636, 3, ["ENSG00000275023"], true, false, false],
["HG00732", 1, 3, 7, false, 38717327, 38719636, 3, ["ENSG00000275023"], false, false, true],
["HG00731", 2, 4, 130, true, 38717327, 38719636, 3, ["ENSG00000275023"], true, false, false],
["HG00732", 1, 3, 70, false, 38717327, 38719636, 3, ["ENSG00000275023"], false, false, true],
["HG00733", null, null, null, null, null, null, null, [], null, null, null]
]
}
Expand All @@ -1625,9 +1625,9 @@
"filters": [],
"sign": 1,
"calls": [
["HG00733", 1, 3, 29, false, 38721781, 38734440, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false],
["HG00733", 1, 3, 290, false, 38721781, 38734440, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false],
["HG00732", null, null, null, null, null, null, null, [], null, null, null],
["HG00731", 1, 3, 28, false, 38721781, 38735703, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false]
["HG00731", 1, 3, 280, false, 38721781, 38735703, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false]
]
}
}, {
Expand Down Expand Up @@ -1686,8 +1686,8 @@
"filters": [],
"sign": 1,
"calls": [
["HG00731", 1, 3, 28, false, 38721781, 38735703, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false],
["HG00733", 1, 3, 29, false, 38721781, 38734440, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false]
["HG00731", 1, 3, 280, false, 38721781, 38735703, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false],
["HG00733", 1, 3, 290, false, 38721781, 38734440, 7, ["ENSG00000275023", "ENSG00000277258", "ENSG00000277972"], false, true, false]
]
}
}, {
Expand Down
8 changes: 4 additions & 4 deletions clickhouse_search/test_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -914,12 +914,12 @@
'genotypes': {
'I000004_hg00731': {
'sampleId': 'HG00731', 'sampleType': 'WES', 'individualGuid': 'I000004_hg00731', 'familyGuid': 'F000002_2',
'numAlt': 2, 'cn': 4, 'qs': 13, 'start': None, 'end': None,
'numAlt': 2, 'cn': 4, 'qs': 130, 'start': None, 'end': None,
'geneIds': None, 'filters': [],
},
'I000005_hg00732': {
'sampleId': 'HG00732', 'sampleType': 'WES', 'individualGuid': 'I000005_hg00732', 'familyGuid': 'F000002_2',
'numAlt': 1, 'cn': 3, 'qs': 7, 'start': None, 'end': None,
'numAlt': 1, 'cn': 3, 'qs': 70, 'start': None, 'end': None,
'geneIds': None, 'filters': [],
},
'I000006_hg00733': {
Expand Down Expand Up @@ -951,7 +951,7 @@
'genotypes': {
'I000004_hg00731': {
'sampleId': 'HG00731', 'sampleType': 'WES', 'individualGuid': 'I000004_hg00731', 'familyGuid': 'F000002_2',
'numAlt': 1, 'cn': 3, 'qs': 28, 'start': None, 'end': None,
'numAlt': 1, 'cn': 3, 'qs': 280, 'start': None, 'end': None,
'geneIds': None, 'filters': [],
},
'I000005_hg00732': {
Expand All @@ -961,7 +961,7 @@
},
'I000006_hg00733': {
'sampleId': 'HG00733', 'sampleType': 'WES', 'individualGuid': 'I000006_hg00733', 'familyGuid': 'F000002_2',
'numAlt': 1, 'cn': 3, 'qs': 29, 'start': None, 'end': 38734440,
'numAlt': 1, 'cn': 3, 'qs': 290, 'start': None, 'end': 38734440,
'geneIds': None, 'filters': [],
}
},
Expand Down
2 changes: 2 additions & 0 deletions seqr/management/commands/tag_seqr_prioritized_variants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@
}
SV_QUALITY_FILTER = {
'min_gq_sv': 90,
'min_qs': 50,
}
PASS_QUALITY_FILTER = {
**QUALITY_FILTER,
Expand All @@ -115,6 +116,7 @@
PERMISSIVE_PASS_QUALITY_FILTER = {
**PASS_QUALITY_FILTER,
'min_gq_sv': 50,
'min_qs': 50,
}

CONFIRMED_HIGH_SPLICE_AI_SEARCH = {
Expand Down
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