bystro-api signup --host https://bystro-dev.emory.edu --email [email protected]
m --password testtest --name "Alex Foo"Response
Signing up for Bystro with email: [email protected], name: Alex Foo
Saved auth credentials to /home/alexkotlar/.bystro/bystro_authentication_token.json:
{
"email": "[email protected]",
"access_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZCI6IjY2M2MwYWJmYTBlMTdhMTY2MGJhODdjNiIsIm5hbWUiOiJBbGV4IEZvbyIsInJvbGUiOiJ1c2VyIiwiZW1haWwiOiJhbGV4dGVzdDJAZ21haWwuY29tIiwiaWF0IjoxNzE1MjEwOTQzLCJleHAiOjE3MTUyMTA5NDR9.LMsjY8JWR7HXQwwaZJbdpW4jSm8jZo_tvijDyxNDse8",
"url": "https://bystro-dev.emory.edu:443"
}
Signup & authentication successful. You may now use the Bystro API!bystro-api get-userResponse
{
"options": {
"autoUploadToS3": false
},
"_id": "663c0abfa0e17a1660ba87c6",
"name": "Alex Foo",
"email": "[email protected]",
"accounts": ["bystro"],
"role": "user"
}bystro-api create-annotation --files /home/alexkotlar/bystro/trio.trim.vep.vcf.bgz --assembly hg19Response
Job creation successful for /home/alexkotlar/bystro/trio.trim.vep.vcf.bgz
{
"assembly": "hg19",
"name": "trio_trim_vep_vcf_bgz-20240508235053964",
"uploadProgress": {
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"error": "",
"progress": 1
},
"options": {
"index": true
},
"inputFileNames": [
"trio.trim.vep.vcf.bgz"
],
"inputQueryConfig": {
"fieldNames": [],
"pipeline": []
},
"search": {
"fieldNames": [],
"archivedSubmissions": [],
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},
"type": "annotation",
"visibility": "private",
"_id": "663c0fdda0e17a1660ba880b",
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"expireDate": "2024-05-15T23:50:53.961Z",
"userId": "663c0abfa0e17a1660ba87c6",
"outputBaseFileName": "trio_trim_vep_vcf_bgz-20240508235053964",
"submission": {
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"_id": "663c0fdea0e17a1660ba880c",
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},
"createdAt": "2024-05-08T23:50:54.078Z",
"updatedAt": "2024-05-08T23:50:54.085Z"
}bystro-api get-jobs --id 663c0fdda0e17a1660ba880bResponse
Fetching job with id: 663c0fdda0e17a1660ba880b
Job(s) fetched successfully:
{
"_id": "663c0fdda0e17a1660ba880b",
"assembly": "hg19",
"name": "trio_trim_vep_vcf_bgz-20240508235053964",
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"uploadProgress": {
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],
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}Here we'll find all mutations that have the sample "4805" as a heterozygote or homozygote.
bystro-api query --job_id 663c0fdda0e17a1660ba880b --query "heteroyzogtes:4805 || homozygotes:4805" | jqResponse
{
"body": {
"took": 2,
"timed_out": false,
"_shards": {
"total": 1,
"successful": 1,
"skipped": 0,
"failed": 0
},
"hits": {
"total": {
"value": 3997,
"relation": "eq"
},
"max_score": 0.49784672,
"hits": [
{
"_index": "663c0fdda0e17a1660ba880b_663c0abfa0e17a1660ba87c6",
"_id": "763",
"_score": 0.49784672,
"_source": {
"caddIndel": {
"alt": [[[null]]],
"PHRED": [[[null]]]
},
"trTv": [[[1]]],
"heterozygosity": [[[0]]],
"homozygotes": [[[1805], [1847], [4805]]],
"refSeq": {
"exonicAlleleFunction": [[["nonSynonymous"]]],
"refAminoAcid": [[["R"]]],
"kgID": [[[null], ["uc002gau.1", "uc002gav.1"]]],
"spDisplayID": [[[null], ["UBP6_HUMAN"]]],
"tRnaName": [[[null]]],
"altAminoAcid": [[["Q"]]],
"codonPosition": [[[2]]],
"strand": [[["+"]]],
"mRNA": [[[null], ["BX647719", "NM_004505"]]],
"protAcc": [[["NP_001291213"], ["NP_004496"]]],
"siteType": [[["exonic"]]],
"codonNumber": [[[912]]],
"name2": [[["USP6"]]],
"spID": [[[null], ["P35125"]]],
"rfamAcc": [[[null]]],
"isCanonical": [[["false"], ["true"]]],
"refCodon": [[["CGG"]]],
"altCodon": [[["CAG"]]],
"name": [[["NM_001304284"], ["NM_004505"]]],
"description": [
[
[null],
[
"Homo sapiens ubiquitin specific peptidase 6 (Tre-2 oncogene) (USP6), mRNA."
]
]
],
"ensemblID": [[[null], ["ENST00000250066", "ENST00000574788"]]]
},
"ref": [[["G"]]],
"inputRef": [[["G"]]],
"homozygosity": [[[1]]],
"an": [[[6]]],
"vcfPos": [[[5058808]]],
"chrom": [[["chr17"]]],
"nearestTss": {
"refSeq": {
"name2": [[["ZNF594"]]],
"name": [[["NM_032530"]]],
"dist": [[[24022]]]
}
},
"dbSNP": {
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"id": [[["rs9899177"]]],
"Vietnamese": [[[0.148900002241135]]],
"GENOME_DK": [[[0.75]]],
"PRJEB37584": [[[null]]],
"Siberian": [[[0.675000011920929]]],
"1000Genomes": [[[0.337099999189377]]],
"dbGaP_PopFreq": [[[0.607900023460388]]],
"HapMap": [[[0.213799998164177]]],
"ExAC": [[[0.508700013160706]]],
"Korea1K": [[[0.10639999806881]]],
"GoNL": [[[0.669300019741058]]],
"TWINSUK": [[[0.642400026321411]]],
"MGP": [[[0.670400023460388]]],
"alt": [[["A"]]],
"TOMMO": [[[0.111599996685982]]],
"NorthernSweden": [[[0.618300020694733]]],
"TOPMED": [[[0.498800009489059]]],
"SGDP_PRJ": [[[0.670099973678589]]],
"Qatari": [[[0.486099988222122]]],
"GnomAD": [[[0.502600014209747]]],
"KOREAN": [[[0.12049999833107]]],
"GoESP": [[[0.52020001411438]]],
"GnomAD_exomes": [[[0.51230001449585]]]
},
"type": [[["SNP"]]],
"heterozygotes": [[[null]]],
"missingness": [[[0]]],
"missingGenos": [[[null]]],
"ac": [[[6]]],
"sampleMaf": [[[1]]],
"clinvarVcf": {
"CLNREVSTAT": [[[null]]],
"CLNSIG": [[[null]]],
"CLNVCSO": [[[null]]],
"SSR": [[[null]]],
"RS": [[[null]]],
"alt": [[[null]]],
"AF_EXAC": [[[null]]],
"AF_TGP": [[[null]]],
"CLNHGVS": [[[null]]],
"CLNDNINCL": [[[null]]],
"CLNSIGCONF": [[[null]]],
"DBVARID": [[[null]]],
"ORIGIN": [[[null]]],
"id": [[[null]]],
"AF_ESP": [[[null]]],
"ALLELEID": [[[null]]],
"CLNDN": [[[null]]]
},
"cadd": [[[23.1]]],
"alt": [[["A"]]],
"id": [[["."]]],
"nearest": {
"refSeq": {
"name2": [[["USP6"]]],
"name": [[["NM_001304284"], ["NM_004505"]]],
"dist": [[[0]]]
}
},
"gnomad": {
"exomes": {
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"AF_nfe_bgr": [[[0.651162981987]]],
"AN_afr": [[[16230]]],
"AN_sas": [[[30568]]],
"AN_nfe_swe": [[[26128]]],
"AN_female": [[[115394]]],
"non_cancer_AN": [[[236618]]],
"controls_AN": [[[109278]]],
"AF_nfe_seu": [[[0.650583028793335]]],
"AF_sas": [[[0.279900997877121]]],
"AN_eas": [[[18374]]],
"AF_eas_kor": [[[0.114053003489971]]],
"AN": [[[251150]]],
"AF_nfe_nwe": [[[0.649953007698059]]],
"AF_eas_jpn": [[[0.0855263024568558]]],
"non_neuro_AF": [[[0.501213014125824]]],
"alt": [[["A"]]],
"AN_amr": [[[34508]]],
"AF": [[[0.512335002422333]]],
"non_cancer_AF": [[[0.508249998092651]]],
"AN_nfe_bgr": [[[2666]]],
"AF_amr": [[[0.561869978904724]]],
"AF_eas": [[[0.165777996182442]]],
"AN_eas_kor": [[[3814]]],
"AF_female": [[[0.514047980308533]]],
"controls_AF": [[[0.493218988180161]]],
"AN_nfe_onf": [[[30962]]],
"non_topmed_AF": [[[0.515302002429962]]],
"non_neuro_AN": [[[207834]]],
"non_topmed_AN": [[[244542]]],
"AF_afr": [[[0.261738002300262]]],
"AF_nfe_onf": [[[0.64327198266983]]],
"AF_nfe_swe": [[[0.648921012878418]]],
"AN_nfe_nwe": [[[42120]]],
"AN_eas_jpn": [[[152]]],
"id": [[["rs9899177"]]]
},
"genomes": {
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"controls_AN": [[[10848]]],
"AN_afr": [[[8682]]],
"AN_asj": [[[288]]],
"alt": [[["A"]]],
"AN_nfe_onf": [[[2134]]],
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"AN_fin": [[[3464]]],
"AN": [[[31312]]],
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"id": [[["rs9899177"]]],
"AN_female": [[[13884]]],
"AF_fin": [[[0.46968799829483]]],
"AF_nfe_seu": [[[0.650942981243134]]],
"AF_afr": [[[0.268487006425858]]],
"AN_amr": [[[846]]],
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"AN_nfe": [[[15390]]],
"AN_oth": [[[1088]]],
"non_neuro_AN": [[[21204]]],
"non_neuro_AF": [[[0.523155987262726]]],
"AN_nfe_seu": [[[106]]],
"AN_nfe_nwe": [[[8576]]],
"AF_asj": [[[0.621528029441833]]],
"AF_oth": [[[0.529411971569061]]],
"AF_female": [[[0.489843994379044]]],
"non_topmed_AF": [[[0.460447996854782]]],
"controls_AF": [[[0.475755989551544]]],
"AF_amr": [[[0.575649976730347]]],
"AF_nfe_nwe": [[[0.641557991504669]]],
"non_topmed_AN": [[[26522]]],
"AF_eas": [[[0.176319003105164]]],
"AF_nfe_est": [[[0.601005971431732]]],
"AF_nfe": [[[0.628849983215332]]]
}
},
"pos": [[[5058808]]],
"discordant": [[["false"]]]
}
}
//....
]
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