EBI-var

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* ENSEMBL variation RDF スキーマ ** https://docs.google.com/drawings/d/1rNMPYPZlWlIhbdhE6GdNrU5-g2F2YpA_wLLsipAzSNs/edit * OWLファイル ** https://github.com/simonjupp/ensembl-rdf/blob/master/ontology/ensembl_variation_ontology.owl * RDF変換スクリプト ** https://github.com/simonjupp/ensembl-rdf/blob/master/scripts/ensemblVariation2ttl.pl * エントリ例 ** http://asia.ensembl.org/Homo_sapiens/Variation/Summary?v=rs766173 * RDF例 ** [[EBI-var/RDF|sample RDF]] * VCFの仕様 ** http://samtools.github.io/hts-specs/VCFv4.1.pdf ** http://samtools.github.io/hts-specs/VCFv4.2.pdf * 菅野研のRDBスキーマ mysql> SHOW COLUMNS FROM vcf_inf_9606_chr22_LC2ad; +--------+------------------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +--------+------------------+------+-----+---------+-------+ | id | int(10) unsigned | NO | PRI | NULL | | | bin | int(10) unsigned | NO | MUL | NULL | | | chr | char(128) | NO | MUL | NULL | | | pos | int(11) | NO | MUL | NULL | | | known | char(64) | YES | | NULL | | | bases | char(16) | NO | | NULL | | | ad | char(64) | NO | | NULL | | | gt | char(32) | NO | | NULL | | | gq | char(64) | NO | | NULL | | | af | char(64) | NO | | NULL | | | info | char(255) | YES | | NULL | | | detail | char(255) | YES | | NULL | | +--------+------------------+------+-----+---------+-------+ 12 rows in set (0.00 sec) * データ例 +----+-----+-------+----------+-------------+-------+-------+-----+-------+------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+ | id | bin | chr | pos | known | bases | ad | gt | gq | af | info | detail | +----+-----+-------+----------+-------------+-------+-------+-----+-------+------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+ | 1 | 10 | chr22 | 15282081 | rs183011531 | G,T | 21,11 | 0/1 | 99 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=1.056;DB;DP=32;Dels=0.00;FS=5.969;HRun=5;HaplotypeScore=0.0000;MQ=37.26;MQ0=3;MQRankSum=-0.427;QD=6.85;ReadPosRankSum=0.607;SB=-54.16 | GT:AD:DP:GQ:PL|0/1:21,11:32:99:249,0,519 | | 2 | 2 | chr22 | 15284670 | rs200510071 | C,T | 13,10 | 0/1 | 53.71 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=2.069;DB;DP=23;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.7340;MQ=30.77;MQ0=5;MQRankSum=0.337;QD=6.41;ReadPosRankSum=0.048;SB=-32.79 | GT:AD:DP:GQ:PL|0/1:13,10:23:53.71:177,0,54 | | 3 | 3 | chr22 | 15284779 | rs146283378 | A,G | 25,11 | 0/1 | 94.83 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=0.689;DB;DP=37;Dels=0.00;FS=9.204;HRun=0;HaplotypeScore=0.5784;MQ=31.26;MQ0=5;MQRankSum=-0.172;QD=1.75;ReadPosRankSum=0.172;SB=-59.75 | GT:AD:DP:GQ:PL|0/1:25,11:37:94.83:95,0,216 | | 4 | 5 | chr22 | 15304362 | rs199959356 | G,T | 38,26 | 0/1 | 99 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=0.230;DB;DP=64;Dels=0.00;FS=1.527;HRun=2;HaplotypeScore=1.5774;MQ=20.89;MQ0=24;MQRankSum=-0.744;QD=2.23;ReadPosRankSum=-0.825;SB=-0.01 | GT:AD:DP:GQ:PL|0/1:38,26:64:99:173,0,131 | | 5 | 4 | chr22 | 15310088 | rs200986103 | G,C | 23,13 | 0/1 | 99 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=-0.103;DB;DP=36;Dels=0.00;FS=1.537;HRun=1;HaplotypeScore=0.8321;MQ=32.36;MQ0=5;MQRankSum=-1.383;QD=2.17;ReadPosRankSum=1.218;SB=-0.01 | GT:AD:DP:GQ:PL|0/1:23,13:36:99:108,0,392 | | 6 | 2 | chr22 | 15310164 | rs200296947 | C,A | 25,22 | 0/1 | 80.17 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=-0.254;DB;DP=47;Dels=0.00;FS=1.830;HRun=0;HaplotypeScore=47.2194;MQ=28.09;MQ0=11;MQRankSum=-1.679;QD=1.07;ReadPosRankSum=2.282;SB=-15.92 | GT:AD:DP:GQ:PL|0/1:25,22:47:80.17:80,0,285 | | 7 | 3 | chr22 | 15315960 | rs201940071 | C,T | 30,21 | 0/1 | 94.82 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=-2.073;DB;DP=51;Dels=0.00;FS=5.036;HRun=0;HaplotypeScore=0.9933;MQ=33.31;MQ0=7;MQRankSum=-1.687;QD=1.27;ReadPosRankSum=-0.096;SB=-0.01 | GT:AD:DP:GQ:PL|0/1:30,21:51:94.82:95,0,573 | | 8 | 3 | chr22 | 15316054 | rs200002043 | T,A | 33,8 | 0/1 | 86.20 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=0.113;DB;DP=41;Dels=0.00;FS=2.006;HRun=2;HaplotypeScore=0.0000;MQ=27.00;MQ0=10;MQRankSum=0.564;QD=1.37;ReadPosRankSum=-2.370;SB=-0.01 | GT:AD:DP:GQ:PL|0/1:33,8:41:86.20:86,0,208 | | 9 | 2 | chr22 | 15316107 | rs202218182 | A,T | 31,14 | 0/1 | 78.18 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=-0.496;DB;DP=46;Dels=0.00;FS=13.239;HRun=1;HaplotypeScore=0.0000;MQ=24.53;MQ0=15;MQRankSum=1.171;QD=4.62;ReadPosRankSum=-1.647;SB=-115.22 | GT:AD:DP:GQ:PL|0/1:31,14:46:78.18:242,0,78 | | 10 | 1 | chr22 | 15316123 | rs200909548 | T,A | 25,14 | 0/1 | 49.21 | 0.50 | AC=1;AF=0.50;AN=2;BaseQRankSum=-0.299;DB;DP=39;Dels=0.00;FS=11.996;HRun=0;HaplotypeScore=0.0000;MQ=25.36;MQ0=14;MQRankSum=0.626;QD=5.71;ReadPosRankSum=0.190;SB=-119.13 | GT:AD:DP:GQ:PL|0/1:25,14:39:49.21:253,0,49 | +----+-----+-------+----------+-------------+-------+-------+-----+-------+------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+

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