News: A Json-Based Annotation Format
2
gravatar for Pierre Lindenbaum
6.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

FYI,

I wrote a java FeatureCodec for JSON with a the tribble library.

See: https://github.com/lindenb/jsontribble

The library contains the tools to sort, index and query the json file.

I also wrote a REST service:

http://localhost:8080/jsontribble/rest/tribble/resources/dbsnp/annotations.json?chrom=chr1&start=881826&end=981826

{"header":{"description":"UCSC  snp137: select count(*) from snp137 where FIND_IN_SET(func,\"missense\")>0 and avHet>0.1"}
,"features":[
{"chrom":"chr1","start":881826,"end":881827,"name":"rs112341375","score":0,"strand":"+","refNCBI":"G","refUCSC":"G","observed":"C/G","class":"single","valid":["by-frequency"],"avHet":0.5,"func":["missense"],"submitters":["BUSHMAN"]}
{"chrom":"chr1","start":897119,"end":897120,"name":"rs28530579","score":0,"strand":"+","refNCBI":"G","refUCSC":"G","observed":"C/G","class":"single","valid":["unknown"],"avHet":0.375,"func":["missense"],"submitters":["ABI","ENSEMBL","SSAHASNP"]}
{"chrom":"chr1","start":907739,"end":907740,"name":"rs112235940","score":0,"strand":"+","refNCBI":"G","refUCSC":"G","observed":"A/G","class":"single","valid":["unknown"],"avHet":0.5,"func":["missense"],"submitters":["COMPLETE_GENOMICS"]}
{"chrom":"chr1","start":949607,"end":949608,"name":"rs1921","score":0,"strand":"+","refNCBI":"G","refUCSC":"G","observed":"A/C/G","class":"single","valid":["by-cluster","by-frequency","by-1000genomes"],"avHet":0.464348,"func":["missense"],"submitters":["1000GENOMES","AFFY","BGI","BUSHMAN","CGAP-GAI","CLINSEQ_SNP","COMPLETE_GENOMICS","CORNELL","DEBNICK","EXOME_CHIP","GMI","HGSV","ILLUMINA","ILLUMINA-UK","KRIBB_YJKIM","LEE","MGC_GENOME_DIFF","NHLBI-ESP","SC_JCM","SC_SNP","SEATTLESEQ","SEQUENOM","UWGC","WIAF","YUSUKE"],"bitfields":["maf-5-some-pop","maf-5-all-pops"]}
]}

Pierre

annotation news genomic index • 1.2k views
ADD COMMENTlink written 6.1 years ago by Pierre Lindenbaum120k
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