EBI-var

提供：TogoWiki

• 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

• エントリ例
  • http://asia.ensembl.org/Homo_sapiens/Variation/Summary?v=rs766173

• RDF例
  • 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 |
+----+-----+-------+----------+-------------+-------+-------+-----+-------+------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+