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Add OurDNA frequency #277

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a35dbe7
Add OurDNA frequency
EddieLF Aug 12, 2025
a078d1e
linting
EddieLF Aug 12, 2025
5653529
linting
EddieLF Aug 12, 2025
600f251
Add ourdna to test fixture data
EddieLF Aug 12, 2025
5e75818
Split into ourdna exomes and genomes
EddieLF Aug 12, 2025
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8 changes: 7 additions & 1 deletion seqr/utils/search/elasticsearch/constants.py
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Expand Up @@ -112,7 +112,13 @@
'AC': 'helix_AC_het',
'AF': 'helix_AF_het',
'max_hl': 'helix_max_hl',
}
},
'ourdna_exomes': {
'filter_AF': 'AF',
},
'ourdna_genomes': {
'filter_AF': 'AF',
},
}

POPULATION_FIELD_CONFIGS = {
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16 changes: 16 additions & 0 deletions seqr/utils/search/elasticsearch/es_utils_tests.py
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Expand Up @@ -869,6 +869,22 @@ def call_request_json(self, index=-1):
'topmed_AF',
'topmed_AN',
'topmed_ID',
'ourdna_exomes_max_hl',
'ourdna_exomes_Hemi',
'ourdna_exomes_Het',
'ourdna_exomes_Hom',
'ourdna_exomes_AC',
'ourdna_exomes_ID',
'ourdna_exomes_AF',
'ourdna_exomes_AN',
'ourdna_genomes_max_hl',
'ourdna_genomes_Hemi',
'ourdna_genomes_Het',
'ourdna_genomes_Hom',
'ourdna_genomes_AC',
'ourdna_genomes_ID',
'ourdna_genomes_AF',
'ourdna_genomes_AN',
'gnomad_genomes_FAF_AF',
'rg37_locus',
'rg37_locus_end',
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2 changes: 2 additions & 0 deletions seqr/views/apis/variant_search_api.py
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Expand Up @@ -209,6 +209,8 @@ def _get_variant_main_transcript_field_val(parsed_variant):
{'header': 'gnomad_genomes_freq', 'value_path': 'populations.gnomad_genomes.af'},
{'header': 'gnomad_exomes_freq', 'value_path': 'populations.gnomad_exomes.af'},
{'header': 'topmed_freq', 'value_path': 'populations.topmed.af'},
{'header': 'ourdna_exomes_freq', 'value_path': 'populations.ourdna_exomes.af'},
{'header': 'ourdna_genomes_freq', 'value_path': 'populations.ourdna_genomes.af'},
{'header': 'cadd', 'value_path': 'predictions.cadd'},
{'header': 'revel', 'value_path': 'predictions.revel'},
{'header': 'eigen', 'value_path': 'predictions.eigen'},
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26 changes: 13 additions & 13 deletions seqr/views/apis/variant_search_api_tests.py
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Expand Up @@ -406,26 +406,26 @@ def test_query_variants(self, mock_get_variants, mock_get_gene_counts, mock_erro
self.assertEqual(response.status_code, 200)
expected_content = [
['chrom', 'pos', 'ref', 'alt', 'gene', 'worst_consequence', 'callset_freq', 'exac_freq', 'gnomad_genomes_freq',
'gnomad_exomes_freq', 'topmed_freq', 'cadd', 'revel', 'eigen', 'splice_ai', 'polyphen', 'sift', 'muttaster', 'fathmm',
'gnomad_exomes_freq', 'topmed_freq', 'ourdna_genomes_freq', 'ourdna_exomes_freq', 'cadd', 'revel', 'eigen', 'splice_ai', 'polyphen', 'sift', 'muttaster', 'fathmm',
'rsid', 'hgvsc', 'hgvsp', 'clinvar_clinical_significance', 'clinvar_gold_stars', 'filter', 'family_id_1',
'tags_1', 'notes_1', 'family_id_2', 'tags_2', 'notes_2', 'sample_1', 'num_alt_alleles_1', 'gq_1', 'ab_1',
'sample_2', 'num_alt_alleles_2', 'gq_2', 'ab_2', 'sample_3', 'num_alt_alleles_3', 'gq_3', 'ab_3'],
['21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '0.13', '', '0.007', '', '', '', '', '', '', '', '', '',
['21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '0.13', '', '0.007', '', '', '', '', '', '', '', '', '', '',
'', '', 'ENST00000623083.3:c.1075G>A', 'ENSP00000485442.1:p.Gly359Ser', '', '', '', '1',
'Tier 1 - Novel gene and phenotype (None)|Review (None)', '', '2', '', '', 'NA19675', '1', '46.0',
'0.702127659574', 'NA19679', '0', '99.0', '0.0', '', '', '', ''],
['3', '835', 'AAAG', 'A', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
['3', '835', 'AAAG', 'A', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
'1', '', '', '', '', '', 'NA19679', '0', '99.0', '0.0', '', '', '', '', '', '', '', ''],
['12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
['12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
'', '2', 'AIP (None)|Known gene for phenotype (None)|Excluded (None)', 'a later note (None)|test n\xf8te (None)', '', '', '', '', '', '',
'', '', '', '', '', '', '', '', ''],
['1', '38724419', 'T', 'G', 'ENSG00000177000', 'missense_variant', '0.31111112236976624', '0.29499998688697815', '0',
'0.28899794816970825', '0.24615199863910675', '20.899999618530273', '0.19699999690055847',
'0.28899794816970825', '0.24615199863910675', '', '20.899999618530273', '0.19699999690055847',
'2.000999927520752', '0.0', '0.1', '0.05', '', '', 'rs1801131', 'ENST00000383791.8:c.156A>C',
'ENSP00000373301.3:p.Leu52Phe', 'Conflicting_classifications_of_pathogenicity', '1', '', '2', '', '', '', '', '', 'HG00731', '2', '99', '1.0',
'HG00732', '1', '99', '0.625', 'HG00733', '0', '40', '0.0'],
['1', '91502721', 'G', 'A', 'ENSG00000097046', 'intron_variant', '0.6666666865348816', '0.0', '0.38041073083877563', '0.0',
'0.36268100142478943', '2.753999948501587', '', '1.378000020980835', '0.009999999776482582', '', '', '',
'0.36268100142478943', '', '2.753999948501587', '', '1.378000020980835', '0.009999999776482582', '', '', '',
'', 'rs13447464', 'ENST00000234626.11:c.-63-251G>A', '', '', '', '', '2', '', '', '', '', '', 'HG00731',
'1', '99', '1.0', 'HG00732', '0', '99', '0.4594594594594595', 'HG00733', '1', '99', '0.4074074074074074'],
]
Expand All @@ -437,29 +437,29 @@ def test_query_variants(self, mock_get_variants, mock_get_gene_counts, mock_erro
self.assertEqual(response.status_code, 200)
expected_content = [
['chrom', 'pos', 'ref', 'alt', 'gene', 'worst_consequence', 'callset_freq', 'exac_freq', 'gnomad_genomes_freq',
'gnomad_exomes_freq', 'topmed_freq', 'cadd', 'revel', 'eigen', 'splice_ai', 'polyphen', 'sift', 'muttaster', 'fathmm',
'gnomad_exomes_freq', 'topmed_freq', 'ourdna_genomes_freq', 'ourdna_exomes_freq', 'cadd', 'revel', 'eigen', 'splice_ai', 'polyphen', 'sift', 'muttaster', 'fathmm',
'rsid', 'hgvsc', 'hgvsp', 'clinvar_clinical_significance', 'clinvar_gold_stars', 'filter', 'family_id_1',
'tags_1', 'notes_1', 'sample_1', 'num_alt_alleles_1', 'gq_1', 'ab_1', 'sample_2', 'num_alt_alleles_2',
'gq_2', 'ab_2', 'sample_3', 'num_alt_alleles_3', 'gq_3', 'ab_3'],
['21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '0.13', '', '0.007', '', '', '', '', '', '', '', '', '', '',
['21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '0.13', '', '0.007', '', '', '', '', '', '', '', '', '', '', '',
'', 'ENST00000623083.3:c.1075G>A', 'ENSP00000485442.1:p.Gly359Ser', '', '', '', '1',
'Tier 1 - Novel gene and phenotype (None)|Review (None)', '', 'NA19675', '1', '46.0', '0.702127659574',
'', '', '', '', '', '', '', '',],
['21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '0.13', '', '0.007', '', '', '', '', '', '', '', '', '', '',
['21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '0.13', '', '0.007', '', '', '', '', '', '', '', '', '', '', '',
'', 'ENST00000623083.3:c.1075G>A', 'ENSP00000485442.1:p.Gly359Ser', '', '', '', '2', '', '',
'NA19679', '0', '99.0', '0.0', '', '', '', '', '', '', '', '',],
['3', '835', 'AAAG', 'A', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
['3', '835', 'AAAG', 'A', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
'1', '', '', 'NA19679', '0', '99.0', '0.0', '', '', '', '', '', '', '', '',],
['12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
['12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
'', '2', 'AIP (None)|Known gene for phenotype (None)|Excluded (None)', 'a later note (None)|test n\xf8te (None)',
'', '', '', '', '', '', '', '', '', '', '', '',],
['1', '38724419', 'T', 'G', 'ENSG00000177000', 'missense_variant', '0.31111112236976624', '0.29499998688697815', '0',
'0.28899794816970825', '0.24615199863910675', '20.899999618530273', '0.19699999690055847',
'0.28899794816970825', '0.24615199863910675', '', '20.899999618530273', '0.19699999690055847',
'2.000999927520752', '0.0', '0.1', '0.05', '', '', 'rs1801131', 'ENST00000383791.8:c.156A>C',
'ENSP00000373301.3:p.Leu52Phe', 'Conflicting_classifications_of_pathogenicity', '1', '', '2', '', '', 'HG00731', '2', '99', '1.0',
'HG00732', '1', '99', '0.625', 'HG00733', '0', '40', '0.0'],
['1', '91502721', 'G', 'A', 'ENSG00000097046', 'intron_variant', '0.6666666865348816', '0.0', '0.38041073083877563', '0.0',
'0.36268100142478943', '2.753999948501587', '', '1.378000020980835', '0.009999999776482582', '', '',
'0.36268100142478943', '', '2.753999948501587', '', '1.378000020980835', '0.009999999776482582', '', '',
'', '', 'rs13447464', 'ENST00000234626.11:c.-63-251G>A', '', '', '', '', '2', '', '', 'HG00731',
'1', '99', '1.0', 'HG00732', '0', '99', '0.4594594594594595', 'HG00733', '1', '99',
'0.4074074074074074'],
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20 changes: 20 additions & 0 deletions seqr/views/utils/test_utils.py
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Expand Up @@ -1104,6 +1104,10 @@ def _get_list_param(call, param):
'filter_af': 0.0009151523074911753, 'het': 0, 'id': None, 'max_hl': None},
'topmed': {'an': 125568, 'ac': 21, 'hom': 0, 'af': 0.00016724, 'hemi': 0, 'filter_af': None, 'het': None,
'id': None, 'max_hl': None},
'ourdna_exomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'ourdna_genomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'sv_callset': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'gnomad_svs': {'ac': None, 'af': None, 'an': None, 'filter_af': None, 'hemi': None, 'hom': None,
Expand Down Expand Up @@ -1187,6 +1191,10 @@ def _get_list_param(call, param):
'filter_af': 0.00016269686320447742, 'het': 0, 'id': None, 'max_hl': None},
'topmed': {'an': 0, 'ac': 0, 'hom': 0, 'af': 0.0, 'hemi': 0, 'filter_af': None, 'het': None, 'id': None,
'max_hl': None},
'ourdna_exomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'ourdna_genomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'sv_callset': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'gnomad_svs': {'ac': None, 'af': None, 'an': None, 'filter_af': None, 'hemi': None, 'hom': None,
Expand Down Expand Up @@ -1272,6 +1280,10 @@ def _get_list_param(call, param):
'id': None, 'max_hl': None},
'topmed': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None, 'het': None,
'id': None, 'max_hl': None},
'ourdna_exomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'ourdna_genomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'sv_callset': {'an': 10088, 'ac': 7, 'hom': None, 'af': 0.000693825, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'gnomad_svs': {'ac': 0, 'af': 0.0, 'an': 0, 'filter_af': None, 'hemi': 0, 'hom': 0, 'het': 0, 'id': None,
Expand Down Expand Up @@ -1357,6 +1369,10 @@ def _get_list_param(call, param):
'id': None, 'max_hl': None},
'topmed': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None, 'het': None,
'id': None, 'max_hl': None},
'ourdna_exomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'ourdna_genomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'sv_callset': {'an': 10088, 'ac': 7, 'hom': None, 'af': 0.000693825, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'gnomad_svs': {'ac': 22, 'af': 0.00679, 'an': 3240, 'filter_af': None, 'hemi': 0, 'hom': 0, 'het': 0,
Expand Down Expand Up @@ -1457,6 +1473,10 @@ def _get_list_param(call, param):
'hemi': None, 'het': None, 'hom': None, 'id': None, 'max_hl': None},
'topmed': {'ac': None, 'af': None, 'an': None, 'filter_af': None, 'hemi': None,
'het': None, 'hom': None, 'id': None, 'max_hl': None},
'ourdna_exomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'ourdna_genomes': {'an': None, 'ac': None, 'hom': None, 'af': None, 'hemi': None, 'filter_af': None,
'het': None, 'id': None, 'max_hl': None},
'callset_heteroplasmy': {'ac': 1, 'af': 0.0003968253968253968, 'an': 2520, 'filter_af': None, 'hemi': None, 'het': None,
'hom': None, 'id': None, 'max_hl': None},
'gnomad_mito_heteroplasmy': {'ac': 3, 'af': 5.317169e-05, 'an': 56421, 'filter_af': None, 'hemi': None, 'het': None,
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12 changes: 12 additions & 0 deletions ui/shared/components/panel/search/constants.js
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Expand Up @@ -432,6 +432,18 @@ export const SNP_FREQUENCIES = [
homHemi: true,
labelHelp: 'Filter by allele count (AC) or by allele frequency (AF) among the samples in this family plus the rest of the samples that were joint-called as part of variant calling for this project.',
},
{
name: 'ourdna_exomes',
label: 'OurDNA exomes',
homHemi: true,
labelHelp: 'Filter by allele count (AC) or allele frequency (AF) in OurDNA exomes',
},
{
name: 'ourdna_genome',
label: 'OurDNA genomes',
homHemi: true,
labelHelp: 'Filter by allele count (AC) or allele frequency (AF) in OurDNA genomes',
},
]

export const MITO_FREQUENCIES = [
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12 changes: 12 additions & 0 deletions ui/shared/components/panel/variants/Frequencies.jsx
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Expand Up @@ -213,6 +213,18 @@ const POPULATIONS = [
queryParams: { [GENOME_VERSION_37]: 'dataset=gnomad_sv_r2_1' },
helpMessage: GNOMAD_SV_CRITERIA_MESSAGE,
},
{
field: 'ourdna_exomes',
fieldTitle: 'OurDNA exomes',
precision: 3,
urls: { [GENOME_VERSION_38]: 'ourdna-dev.popgen.rocks', },
},
{
field: 'ourdna_genomes',
fieldTitle: 'OurDNA genomes',
precision: 3,
urls: { [GENOME_VERSION_38]: 'ourdna-dev.popgen.rocks', },
},
]

const CALLSET_HET_POP = {
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2 changes: 2 additions & 0 deletions ui/shared/utils/constants.js
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Expand Up @@ -1616,6 +1616,8 @@ export const VARIANT_EXPORT_DATA = [
{ header: 'gnomad_genomes_freq', getVal: getPopAf('gnomad_genomes') },
{ header: 'gnomad_exomes_freq', getVal: getPopAf('gnomad_exomes') },
{ header: 'topmed_freq', getVal: getPopAf('topmed') },
{ header: 'ourdna_exomes_freq', getVal: getPopAf('ourdna_exomes') },
{ header: 'ourdna_genomes_freq', getVal: getPopAf('ourdna_genomes') },
{ header: 'cadd', getVal: variant => (variant.predictions || {}).cadd },
{ header: 'revel', getVal: variant => (variant.predictions || {}).revel },
{ header: 'eigen', getVal: variant => (variant.predictions || {}).eigen },
Expand Down
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