Skip to content

Latest commit

 

History

History
118 lines (74 loc) · 3.17 KB

query-logs.md

File metadata and controls

118 lines (74 loc) · 3.17 KB
Raw

Notes on query logs

server=gwas-api.mrcieu.ac.uk

phewas_rsid

PheWAS query using rsid

  • searches the entire set of records using list of SNP IDs and P-value filter

API function name:

  • elastic_query_phewas_rsid

API:

  • curl -XGET "http://$server/phewas/rs4343/0.001"

Log:

  • name:phewas_rsid time:0.5915 hits:84 rsid:['rs4343'] pval:0.001 indexes:['prot-c',.....]

phewas_chrpos

PheWAS query using chromosome and position

  • searches the entire set of records using chromosome name and base position

API function name:

  • elastic_query_phewas_chrpos

API:

  • curl -XGET "http://$server/phewas/7%3A105561135/0.001"

Log:

  • name:phewas_chrpos time1.2809 hits:11 chrpos:[{'chr': 7, 'start': 105561135, 'end': 105561135, 'type': 'position', 'orig': '7:105561135'}] pval:0.001 indexes:['prot-c',...]

phewas_cprange

PheWAS query using chromosome and poistion range

  • searches the entire set of records uing chromosome name and range

API function name:

  • elastic_query_phewas_cprange

API:

  • curl -XGET "http://$server/phewas/7%3A105561135-105563135/0.001"

Log:

  • name:phewas_cprange time:2.1037 hits:208 cprange:[{'chr': 7, 'start': 105561135, 'end': 105563135, 'type': 'range', 'orig': '7:105561135-105563135'}] pval:0.001 indexes:['prot-c',...]

chrpos

Standard query using list of GWAS IDs, chromosome and position

  • searches specific GWAS using chromosome name and base position

API function name:

  • elastic_query_chrpos

API:

  • curl -XGET "http://$server/associations/ieu-a-1/3%3A186461181"

Log:

  • name:chrpos time:0.0336 hits:1 chrpos:[{'chr': 3, 'start': 186461181, 'end': 186461181, 'type': 'position', 'orig': '6:186461181'}] gwas:['ieu-a-1'] indexes:{'ieu-a': ['1']}

cprange

Standard query using list of GWAS IDs, chromosome position and range

  • searches specific GWAS using chromosome position and range

API function name:

  • elastic_query_cprange

API:

  • curl -XGET "http://$server/associations/ieu-a-1/7%3A105561135-105563135"

Log:

  • name:cprange time:0.4407 hits:3099 cprange:[{'chr': 7, 'start': 105561135, 'end': 105563135, 'type': 'range', 'orig': '7:105561135-105563135'}] gwas['ieu-a-1'] indexes{'ieu-a': ['1']}

rsid

Standard query using list of GWAS IDs and list of SNP IDs

  • searches specific GWAS and SNPs

API function name:

  • elastic_query_rsid

API:

  • curl -XGET "http://$server/associations/finn-a-C3_CORPUS_UTERI/rs75438046,rs1808192"

Log:

  • name:rsid time:0.0328 hits:1 rsid:['rs75438046', 'rs1808192'] gwas:['finn-a-C3_CORPUS_UTERI'] indexes:{'finn-a': ['C3_CORPUS_UTERI']}

pval

Tophits query searching separate set of tophits data

  • the tophits data set is a very small curated subset of all data

API function name:

  • elastic_query_pval

API:

  • curl -X POST "http://$server/tophits?id=ieu-a-1&pval=0.0001&preclumped=1&clump=1&bychr=1&r2=0.001&kb=5000&pop=EUR" -H "accept: application/json" -H "X-Api-Token: null"

Log:

  • name:pval time:0.4632 hits:14 pval:1e-04 gwas:['ieu-a-1'] indexes:{'ieu-a': ['1']}

Example call frequencies

~250k queries

  • rsid: 181396
  • cprange: 41331
  • pval: 11268
  • phewas_rsid: 736
  • chrpos: 93
  • phewas_chrpos: 7
  • phewas_cprange: 6