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query details: referenceName, maximum number of variants in a beacon, multi variation queries #349

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albodrug opened this issue Jul 8, 2024 · 1 comment

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@albodrug
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albodrug commented Jul 8, 2024

Hello,

I have several questions regarding the ri, as my queries don't behave as I would expect them to.

  1. Is there a way in beacon2-ri to specify the reference sequence name as specified in the beacon specifications. My queries on g_variations work unless I specify the "referenceName"
Finds no variation with referenceName specified

(itx)> curl -H 'Content-Type: application/json' -X POST -d '{
"meta": {
"apiVersion": "2.0"
},
"query": {
"requestParameters": {
"referenceName" : "1",
"alternateBases": "G" ,
"referenceBases": "A" ,
"start": [ 16050074 ],
"end": [ 16050568 ],
"variantType": "SNP"
},
"filters": [],
"includeResultsetResponses": "HIT",
"pagination": {
"skip": 0,
"limit": 10
},
"testMode": false,
"requestedGranularity": "count"
}
}' http://localhost:5050/api/g_variants
{"meta":{"beaconId":"itx.french.beacon","apiVersion":"v2.0.1","returnedGranularity":"count","receivedRequestSummary":{"apiVersion":"2.0","requestedSchemas":[],"filters":[],"requestParameters":{"referenceName":"1","alternateBases":"G","referenceBases":"A","start":[16050074],"end":[16050568],"variantType":"SNP"},"includeResultsetResponses":"HIT","pagination":{"skip":0,"limit":10},"requestedGranularity":"count","testMode":false},"returnedSchemas":[{"entityType":"genomicVariation","schema":"beacon-g_variant-v2.0.0"}]},"responseSummary":{"exists":false,"numTotalResults":0},"beaconHandovers":[{"handoverType":{"id":"CUSTOM:000001","label":"Project description"},"note":"Project description","url":"https://www.nist.gov/programs-projects/genome-bottle"}]}

Finds 6 variations, only difference is no referenceName specified. Variations are in different chromosomes.

(itx)> curl -H 'Content-Type: application/json' -X POST -d '{
"meta": {
"apiVersion": "2.0"
},
"query": {
"requestParameters": {
"alternateBases": "G" ,
"referenceBases": "A" ,
"start": [ 16050074 ],
"end": [ 16050568 ],
"variantType": "SNP"
},
"filters": [],
"includeResultsetResponses": "HIT",
"pagination": {
"skip": 0,
"limit": 10
},
"testMode": false,
"requestedGranularity": "record"
}
}' http://localhost:5050/api/g_variants | python -m json.tool
{
"meta": {
"beaconId": "itx.french.beacon",
"apiVersion": "v2.0.1",
"returnedGranularity": "record",
"receivedRequestSummary": {
"apiVersion": "2.0",
"requestedSchemas": [],
"filters": [],
"requestParameters": {
"alternateBases": "G",
"referenceBases": "A",
"start": [
16050074
],
"end": [
16050568
],
"variantType": "SNP"
},
"includeResultsetResponses": "HIT",
"pagination": {
"skip": 0,
"limit": 10
},
"requestedGranularity": "record",
"testMode": false
},
"returnedSchemas": [
{
"entityType": "genomicVariation",
"schema": "beacon-g_variant-v2.0.0"
}
]
},
"responseSummary": {
"exists": true,
"numTotalResults": 6
},
"response": {
"resultSets": [
{
"id": "1kGP_DATASET_3K",
"setType": "dataset",
"exists": true,
"resultsCount": 6,
"results": [
{
"_id": "6687c06cb7605e6f09067ef6",
"_info": {
"datasetId": "default_beacon_1",
"vcf2bff": {
"version": "2.0.0",
"cwd": "/home/bodrug-a/Devlopment/beacon2-ri-tools/beacon_172000971995122/vcf",
"ncpuhost": "20",
"filein": "WGS_chr1_to_chr10.norm.ann.dbnsfp.clinvar.cosmic.vcf.gz",
"user": "bodrug-a",
"hostname": "pp-irs1-4071ylt",
"projectDir": "beacon_172000971995122",
"fileout": "genomicVariationsVcf.json.gz"
},
"genome": "hg38"
},
"variation": {
"referenceBases": "A",
"variantType": "SNP",
"alternateBases": "G",
"location": {
"sequence_id": "HGVSid:chr2:g.16050460A>G",
"interval": {
"type": "SequenceInterval",
"end": {
"value": 16050460,
"type": "Number"
},
"start": {
"type": "Number",
"value": 16050459
}
},
"type": "SequenceLocation"
}
},
"molecularAttributes": {
"annotationImpact": [
"MODIFIER",
"MODIFIER",
"MODIFIER",
"MODIFIER"
],
"geneIds": [
"AC010145.1",
"GACAT3",
"GACAT3",
"GACAT3"
],
"molecularEffects": [
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"label": "non_coding_transcript_exon_variant",
"id": "ENSGLOSSARY:0000160"
}
],
"aminoacidChanges": [
".",
".",
".",
"."
]
},
"variantQuality": {
"QUAL": 0,
"FILTER": "PASS"
},
"identifiers": {
"genomicHGVSId": "chr2:g.16050460A>G"
},
"_position": {
"startInteger": 16050459,
"endInteger": 16050460,
"assemblyId": "hg38",
"refseqId": "2",
"start": [
16050459
],
"end": [
16050460
]
},
"variantInternalId": "chrchr2_16050460_A_G",
"caseLevelData": [
{
"biosampleId": "HG03575",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"biosampleId": "HG03576",
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
}
}
]
},
{
"_id": "6687c06cb7605e6f09067f11",
"_info": {
"genome": "hg38",
"datasetId": "default_beacon_1",
"vcf2bff": {
"cwd": "/home/bodrug-a/Devlopment/beacon2-ri-tools/beacon_172000971995122/vcf",
"version": "2.0.0",
"projectDir": "beacon_172000971995122",
"fileout": "genomicVariationsVcf.json.gz",
"hostname": "pp-irs1-4071ylt",
"ncpuhost": "20",
"filein": "WGS_chr1_to_chr10.norm.ann.dbnsfp.clinvar.cosmic.vcf.gz",
"user": "bodrug-a"
}
},
"molecularAttributes": {
"aminoacidChanges": [
"",
".",
".",
"."
],
"molecularEffects": [
{
"id": "ENSGLOSSARY:0000164",
"label": "upstream_gene_variant"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"id": "ENSGLOSSARY:0000161",
"label": "intron_variant"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
}
],
"geneIds": [
"GACAT3",
"AC010145.1",
"GACAT3",
"GACAT3"
],
"annotationImpact": [
"MODIFIER",
"MODIFIER",
"MODIFIER",
"MODIFIER"
]
},
"variation": {
"location": {
"interval": {
"type": "SequenceInterval",
"end": {
"value": 16050396,
"type": "Number"
},
"start": {
"type": "Number",
"value": 16050395
}
},
"type": "SequenceLocation",
"sequence_id": "HGVSid:chr2:g.16050396A>G"
},
"alternateBases": "G",
"referenceBases": "A",
"variantType": "SNP"
},
"identifiers": {
"genomicHGVSId": "chr2:g.16050396A>G"
},
"variantQuality": {
"FILTER": "PASS",
"QUAL": 0
},
"caseLevelData": [
{
"biosampleId": "HG00103",
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
}
},
{
"biosampleId": "NA20899",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA20905"
},
{
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "1|0"
},
"biosampleId": "NA20906"
},
{
"biosampleId": "NA21088",
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
}
},
{
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA21102"
},
{
"biosampleId": "NA21111",
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
}
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA21116"
},
{
"biosampleId": "NA21118",
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
}
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA21124"
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA21126"
},
{
"biosampleId": "NA21133",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
}
],
"_position": {
"start": [
16050395
],
"end": [
16050396
],
"refseqId": "2",
"assemblyId": "hg38",
"endInteger": 16050396,
"startInteger": 16050395
},
"variantInternalId": "chrchr2_16050396_A_G"
},
{
"_id": "6687b6f0b7605e6f09aeb455",
"variantInternalId": "chrchr1_16050251_A_G",
"_position": {
"assemblyId": "hg38",
"endInteger": 16050251,
"startInteger": 16050250,
"start": [
16050250
],
"end": [
16050251
],
"refseqId": "1"
},
"caseLevelData": [
{
"biosampleId": "HG00252",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
}
],
"_info": {
"genome": "hg38",
"datasetId": "default_beacon_1",
"vcf2bff": {
"version": "2.0.0",
"cwd": "/home/bodrug-a/Devlopment/beacon2-ri-tools/beacon_172000971995122/vcf",
"user": "bodrug-a",
"filein": "WGS_chr1_to_chr10.norm.ann.dbnsfp.clinvar.cosmic.vcf.gz",
"ncpuhost": "20",
"hostname": "pp-irs1-4071ylt",
"fileout": "genomicVariationsVcf.json.gz",
"projectDir": "beacon_172000971995122"
}
},
"variation": {
"referenceBases": "A",
"variantType": "SNP",
"location": {
"interval": {
"type": "SequenceInterval",
"end": {
"type": "Number",
"value": 16050251
},
"start": {
"type": "Number",
"value": 16050250
}
},
"type": "SequenceLocation",
"sequence_id": "HGVSid:chr1:g.16050251A>G"
},
"alternateBases": "G"
},
"molecularAttributes": {
"molecularEffects": [
{
"label": "upstream_gene_variant",
"id": "ENSGLOSSARY:0000164"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"id": "ENSGLOSSARY:0000161",
"label": "intron_variant"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
}
],
"aminoacidChanges": [
"",
".",
".",
"."
],
"annotationImpact": [
"MODIFIER",
"MODIFIER",
"MODIFIER",
"MODIFIER"
],
"geneIds": [
"CLCNKB",
"CLCNKB",
"CLCNKB",
"CLCNKB"
]
},
"variantQuality": {
"FILTER": "PASS",
"QUAL": 0
},
"identifiers": {
"genomicHGVSId": "chr1:g.16050251A>G"
}
},
{
"_id": "6687b6f0b7605e6f09aeb474",
"_position": {
"startInteger": 16050223,
"assemblyId": "hg38",
"endInteger": 16050224,
"refseqId": "1",
"start": [
16050223
],
"end": [
16050224
]
},
"variantInternalId": "chrchr1_16050224_A_G",
"caseLevelData": [
{
"biosampleId": "HG00096",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"biosampleId": "HG00097",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
},
"biosampleId": "HG00099"
},
{
"biosampleId": "HG00100",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
},
"biosampleId": "HG00101"
},
{
"biosampleId": "HG00561",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"biosampleId": "HG00565",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"biosampleId": "HG00566",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
},
"biosampleId": "HG00567"
},
{
"biosampleId": "HG00577",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"biosampleId": "HG02120",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
},
"biosampleId": "HG02121"
},
{
"biosampleId": "HG02122",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"biosampleId": "NA12718",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"biosampleId": "NA12739",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"biosampleId": "NA19068",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
},
"biosampleId": "NA19070"
},
{
"biosampleId": "NA19072",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
},
{
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
},
"biosampleId": "NA19074"
},
{
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
},
"biosampleId": "NA19902"
},
{
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA19904"
},
{
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA19908"
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA19909"
},
{
"biosampleId": "NA19913",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
},
"biosampleId": "NA19914"
},
{
"biosampleId": "NA21141",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
},
"biosampleId": "NA21142"
},
{
"biosampleId": "NA21143",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
},
{
"biosampleId": "NA21144",
"zygosity": {
"label": "1|1",
"id": "GENO:GENO_0000136"
}
}
],
"variantLevelData": {
"clinicalInterpretations": [
{
"category": {
"id": "MONDO:0000001",
"label": "disease or disorder"
},
"clinicalRelevance": "benign",
"effect": {
"label": "not_provided",
"id": "MedGen:CN517202"
},
"annotatedWith": {
"toolName": "SnpEff",
"toolReferences": {
"bio.toolsId": "https://bio.tools/snpeff",
"databases": {
"COSMIC": {
"version": "COSMICv92",
"url": "https://cosmic-blog.sanger.ac.uk/cosmic-release-v92"
},
"ClinVar": {
"version": "20211218",
"url": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2021"
},
"dbSNSFP": {
"url": "https://sites.google.com/site/jpopgen/dbNSFP",
"version": "dbNSFP4.1a"
}
},
"url": "https://pcingola.github.io/SnpEff"
},
"version": "5.0"
},
"conditionId": "not_provided"
}
]
},
"_info": {
"genome": "hg38",
"vcf2bff": {
"filein": "WGS_chr1_to_chr10.norm.ann.dbnsfp.clinvar.cosmic.vcf.gz",
"user": "bodrug-a",
"ncpuhost": "20",
"hostname": "pp-irs1-4071ylt",
"fileout": "genomicVariationsVcf.json.gz",
"projectDir": "beacon_172000971995122",
"version": "2.0.0",
"cwd": "/home/bodrug-a/Devlopment/beacon2-ri-tools/beacon_172000971995122/vcf"
},
"datasetId": "default_beacon_1"
},
"variation": {
"referenceBases": "A",
"variantType": "SNP",
"alternateBases": "G",
"location": {
"sequence_id": "HGVSid:NC_000001.11:g.16050224A>G",
"type": "SequenceLocation",
"interval": {
"end": {
"value": 16050224,
"type": "Number"
},
"start": {
"type": "Number",
"value": 16050223
},
"type": "SequenceInterval"
}
}
},
"molecularAttributes": {
"molecularEffects": [
{
"id": "ENSGLOSSARY:0000164",
"label": "upstream_gene_variant"
},
{
"id": "ENSGLOSSARY:0000161",
"label": "intron_variant"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
}
],
"aminoacidChanges": [
"",
".",
".",
"."
],
"annotationImpact": [
"MODIFIER",
"MODIFIER",
"MODIFIER",
"MODIFIER"
],
"geneIds": [
"CLCNKB",
"CLCNKB",
"CLCNKB",
"CLCNKB"
]
},
"variantQuality": {
"QUAL": 0,
"FILTER": "PASS"
},
"identifiers": {
"genomicHGVSId": "NC_000001.11:g.16050224A>G"
}
},
{
"_id": "6687c06cb7605e6f09067eef",
"caseLevelData": [
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "HG04191"
},
{
"biosampleId": "HG04192",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "1|0"
}
},
{
"biosampleId": "HG04193",
"zygosity": {
"id": "GENO:GENO_0000136",
"label": "1|1"
}
}
],
"_position": {
"refseqId": "2",
"start": [
16050186
],
"end": [
16050187
],
"startInteger": 16050186,
"endInteger": 16050187,
"assemblyId": "hg38"
},
"variantInternalId": "chrchr2_16050187_A_G",
"_info": {
"vcf2bff": {
"version": "2.0.0",
"cwd": "/home/bodrug-a/Devlopment/beacon2-ri-tools/beacon_172000971995122/vcf",
"filein": "WGS_chr1_to_chr10.norm.ann.dbnsfp.clinvar.cosmic.vcf.gz",
"user": "bodrug-a",
"ncpuhost": "20",
"hostname": "pp-irs1-4071ylt",
"projectDir": "beacon_172000971995122",
"fileout": "genomicVariationsVcf.json.gz"
},
"datasetId": "default_beacon_1",
"genome": "hg38"
},
"identifiers": {
"genomicHGVSId": "chr2:g.16050187A>G"
},
"variantQuality": {
"QUAL": 0,
"FILTER": "PASS"
},
"molecularAttributes": {
"annotationImpact": [
"MODIFIER",
"MODIFIER",
"MODIFIER",
"MODIFIER"
],
"geneIds": [
"GACAT3",
"AC010145.1",
"GACAT3",
"GACAT3"
],
"molecularEffects": [
{
"id": "ENSGLOSSARY:0000164",
"label": "upstream_gene_variant"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"id": "ENSGLOSSARY:0000161",
"label": "intron_variant"
},
{
"id": "ENSGLOSSARY:0000161",
"label": "intron_variant"
}
],
"aminoacidChanges": [
"",
".",
".",
"."
]
},
"variation": {
"variantType": "SNP",
"referenceBases": "A",
"alternateBases": "G",
"location": {
"sequence_id": "HGVSid:chr2:g.16050187A>G",
"interval": {
"type": "SequenceInterval",
"end": {
"type": "Number",
"value": 16050187
},
"start": {
"value": 16050186,
"type": "Number"
}
},
"type": "SequenceLocation"
}
}
},
{
"_id": "6687b6f0b7605e6f09aeb454",
"variantInternalId": "chrchr1_16050120_A_G",
"_position": {
"endInteger": 16050120,
"assemblyId": "hg38",
"startInteger": 16050119,
"end": [
16050120
],
"start": [
16050119
],
"refseqId": "1"
},
"caseLevelData": [
{
"biosampleId": "HG01884",
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
}
},
{
"biosampleId": "HG01889",
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
}
},
{
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
},
"biosampleId": "HG01956"
},
{
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
},
"biosampleId": "HG02281"
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "HG02464"
},
{
"biosampleId": "HG02973",
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
}
},
{
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
},
"biosampleId": "HG02975"
},
{
"biosampleId": "HG03052",
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
}
},
{
"biosampleId": "HG03081",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
},
"biosampleId": "HG03270"
},
{
"biosampleId": "HG03272",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"biosampleId": "HG03279",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"biosampleId": "HG03578",
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
}
},
{
"biosampleId": "NA18871",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "1|0"
},
"biosampleId": "NA18872"
},
{
"biosampleId": "NA19025",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA19036"
},
{
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "1|0"
},
"biosampleId": "NA19113"
},
{
"biosampleId": "NA19115",
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
}
},
{
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "1|0"
},
"biosampleId": "NA19346"
},
{
"biosampleId": "NA19383",
"zygosity": {
"label": "1|0",
"id": "GENO:GENO_0000458"
}
},
{
"biosampleId": "NA19395",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"biosampleId": "NA19438",
"zygosity": {
"id": "GENO:GENO_0000458",
"label": "0|1"
}
},
{
"zygosity": {
"label": "0|1",
"id": "GENO:GENO_0000458"
},
"biosampleId": "NA19473"
}
],
"_info": {
"datasetId": "default_beacon_1",
"vcf2bff": {
"cwd": "/home/bodrug-a/Devlopment/beacon2-ri-tools/beacon_172000971995122/vcf",
"version": "2.0.0",
"fileout": "genomicVariationsVcf.json.gz",
"projectDir": "beacon_172000971995122",
"hostname": "pp-irs1-4071ylt",
"ncpuhost": "20",
"filein": "WGS_chr1_to_chr10.norm.ann.dbnsfp.clinvar.cosmic.vcf.gz",
"user": "bodrug-a"
},
"genome": "hg38"
},
"variation": {
"alternateBases": "G",
"location": {
"sequence_id": "HGVSid:chr1:g.16050120A>G",
"interval": {
"start": {
"value": 16050119,
"type": "Number"
},
"end": {
"type": "Number",
"value": 16050120
},
"type": "SequenceInterval"
},
"type": "SequenceLocation"
},
"variantType": "SNP",
"referenceBases": "A"
},
"molecularAttributes": {
"molecularEffects": [
{
"id": "ENSGLOSSARY:0000164",
"label": "upstream_gene_variant"
},
{
"id": "ENSGLOSSARY:0000161",
"label": "intron_variant"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
},
{
"label": "intron_variant",
"id": "ENSGLOSSARY:0000161"
}
],
"aminoacidChanges": [
"",
".",
".",
"."
],
"annotationImpact": [
"MODIFIER",
"MODIFIER",
"MODIFIER",
"MODIFIER"
],
"geneIds": [
"CLCNKB",
"CLCNKB",
"CLCNKB",
"CLCNKB"
]
},
"variantQuality": {
"QUAL": 0,
"FILTER": "PASS"
},
"identifiers": {
"genomicHGVSId": "chr1:g.16050120A>G"
}
}
],
"resultsHandover": {
"handoverType": {
"id": "CUSTOM:000001",
"label": "Project description"
},
"note": "Project description",
"url": "https://www.nist.gov/programs-projects/genome-bottle"
}
}
]
},
"beaconHandovers": [
{
"handoverType": {
"id": "CUSTOM:000001",
"label": "Project description"
},
"note": "Project description",
"url": "https://www.nist.gov/programs-projects/genome-bottle"
}
]
}

  1. Are there any limitations on the number of variations the beacon2-ri-tools or ri-api can load? I have 70M variant positions in my dataset, all my 70M positions have an alternate allele in at least one biosample. Once converted to bff using ri-tools, i am left with only 10M variants. I am using the v1 of ri-tools because I cannot make ri-tools-v2 work.

  2. Finally, my last question: is there a way in beacon to query for individuals or biosamples that have several specified variations. So, not specifying one single position or one single range for variations, but two or more. For example, with several queries:

curl
-H 'Content-Type: application/json'
-X POST
-d '{
"meta": {
"apiVersion": "2.0"
},
"query": {
"requestParameters": {
"alternateBases": "G" ,
"referenceBases": "A" ,
"start": [ 16050074 ],
"end": [ 16050568 ],
"variantType": "SNP"
},
"query": {
"requestParameters": {
"alternateBases": "G" ,
"referenceBases": "A" ,
"start": [ 50074 ],
"end": [ 150568 ],
"variantType": "SNP"
},
"filters": [],
"includeResultsetResponses": "HIT",
"pagination": {
"skip": 0,
"limit": 10
},
"testMode": false,
"requestedGranularity": "record"
}
}'
http://localhost:5050/api/g_variants

Thanks for any insights or tips!
Have a nice day,
Alex

@costero-e
Copy link
Collaborator

Hi @albodrug ,
thanks for reporting this. Let's go with the questions:

  1. In beacon2-ri-api, you can specify the referenceName as the specifications, with two possible ways of doing it:
    g_variants?referenceName=22
    or
    g_variants?referenceName=NC_000022.11
    In any case, you need to have the identifiers.genomicHGVSId correctly filled in.
  2. I didn't understand what exactly is your issue, but beacon ri tools v2 doesn't have any limit on the number of variants to transform neither does the API in the number of variants you can load. If the issue is with tools v1, we are not mantaining that software anymore (at least in EGA). If you tell me why you can't make tools v2 work I can help you (start an issue there).
  3. In the specifications, right now, this is not possible. There are range queries or bracket queries, but if you want two specific range queries or bracket queries at the same time, you will have to do them one by one. Once said that, in beacon2 RI API I have this implemented (out of the spec) by sending an array of request parameters, like this:
    curl \ -H 'Content-Type: application/json' \ -X POST \ -d '{ "meta": { "apiVersion": "2.0" }, "query": { "requestParameters": [{ "alternateBases": "G" , "referenceBases": "A" , "start": [ 16050074 ], "end": [ 16050568 ], "variantType": "SNP"},{ "alternateBases": "G" , "referenceBases": "A" , "start": [ 50074 ], "end": [ 150568 ], "variantType": "SNP"}], "includeResultsetResponses": "HIT", "pagination": { "skip": 0, "limit": 10 }, "testMode": false, "requestedGranularity": "record" } }' \ http://localhost:5050/api/individuals

Best,

Oriol

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