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Commit message:
Uploaded |
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added:
test-data/regions.bed test-data/slice_in.vcf test-data/slice_out.vcf tool_dependencies.xml vcftools_slice.xml |
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| diff -r 000000000000 -r 1363e5d4a8b8 test-data/regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regions.bed Sun Nov 24 17:12:15 2013 -0500 |
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| @@ -0,0 +1,2 @@ +chr1 18960722 47767914 +chr1 65321419 85742338 \ No newline at end of file |
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| diff -r 000000000000 -r 1363e5d4a8b8 test-data/slice_in.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slice_in.vcf Sun Nov 24 17:12:15 2013 -0500 |
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| b'@@ -0,0 +1,76 @@\n+##fileformat=VCFv4.1\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tpanc1_ng\n+chr1\t2985885\t.\tC\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:70:64:48:16:25%:9.8E-1:34:20:0:48:0:16\n+chr1\t3301721\t.\tC\tT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:687:619:205:414:66.77%:9.8E-1:35:24:130:75:279:135\n+chr1\t3328358\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:314:278:0:278:100%:9.8E-1:0:25:0:0:131:147\n+chr1\t3328659\t.\tC\tT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:417:362:294:68:18.78%:9.8E-1:35:19:110:184:35:33\n+chr1\t3329384\t.\tC\tT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:161:147:119:28:19.05%:9.8E-1:33:26:32:87:6:22\n+chr1\t3350409\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:567:471:157:314:66.67%:9.8E-1:33:25:75:82:180:134\n+chr1\t3352161\t.\tT\tTA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:511:467:362:105:22.29%:9.8E-1:34:33:167:195:59:46\n+chr1\t3352227\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:645:447:1:446:99.78%:9.8E-1:26:32:0:1:256:190\n+chr1\t3352347\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:517:427:0:427:100%:9.8E-1:0:34:0:0:126:301\n+chr1\t3352503\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:449:304:0:303:100%:9.8E-1:0:19:0:0:170:133\n+chr1\t3352541\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:466:401:0:401:100%:9.8E-1:0:25:0:0:189:212\n+chr1\t3352579\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:533:482:0:482:100%:9.8E-1:0:24:0:0:231:251\n+chr1\t3352763\t.\tCT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:437:369:248:112:29.32%:9.8E-1:33:31:143:105:62:50\n+chr1\t3352784\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:443:357:253:104:29.05%:9.8E-1:30:25:160:93:54:50\n+chr1\t3352872\t.\tA\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:590:471:333:138:29.3%:9.8E-1:33:22:247:86:104:34\n+chr1\t3353890\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:478:430:0:429:99.77%:9.8E-1:0:34:0:0:242:187\n+chr1\t3353949\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:690:621:0:620:99.84%:9.8E-1:0:22:0:0:421:199\n+chr1\t3354595\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:519:461:3:458:99.35%:9.8E-1:30:19:0:3:197:261\n+chr1\t3354615\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:495:459:0:459:100%:9.8E-1:0:19:0:0:220:239\n+chr1\t18960722\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:701:648:489:159:24.54%:9.8E-1:34:22:346:143:121:38\n+chr1\t19071752\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:770:715:219:495:69.23%:9.8E-1:35:21:86:133:184:311\n+chr1\t19071865\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:517:479:174:305:63.54%:9.8E-1:35:34:42:132:91:214\n+chr1\t19072808\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:706:657:228:429:65.3%:9.8E-1:36:19:99:129:197:232\n+chr1\t19072926\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:673:618:183:435:70.39%:9.8E-1:35:24:96:87:187:248\n+chr1\t19074980\t.\tC\tT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:720:676:221:454:67.06%:9.8E-1:35:35:89:132:226:228\n+chr1\t19075225\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:718:660:190:468:70.91%:9.8E-1:34:34:93:97:231:237\n+chr1\t19075327\t.\tC\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:623:588:178:410:69.73%:9.8E-1:36:36:63:115:142:268\n+chr1\t36752152\t.\tC\tT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:845:780:216:564:72.31%:9.8E-1:36:25:103:113:249:315\n+chr1\t36759426\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:504:465:152'..b':65:70\n+chr1\t47735280\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:414:381:98:283:74.28%:9.8E-1:35:36:74:24:225:58\n+chr1\t47767914\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:560:533:377:156:29.27%:9.8E-1:35:34:222:155:91:65\n+chr1\t51433821\t.\tG\tGC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:454:407:44:394:89.34%:9.8E-1:33:32:12:32:88:306\n+chr1\t51433863\t.\tG\tGC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:373:318:23:317:92.96%:9.8E-1:33:31:3:20:70:247\n+chr1\t51433888\t.\tA\tAG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:343:284:34:287:87.77%:9.8E-1:33:29:3:31:85:202\n+chr1\t51822188\t.\tGA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:406:277:226:29:10.25%:9.8E-1:34:30:164:62:18:11\n+chr1\t51873951\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:773:740:521:219:29.59%:9.8E-1:37:37:189:332:88:131\n+chr1\t59248813\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:463:412:0:412:100%:9.8E-1:0:33:0:0:80:332\n+chr1\t59249031\t.\tT\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:284:249:0:249:100%:9.8E-1:0:22:0:0:103:146\n+chr1\t59249347\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:320:278:1:276:99.28%:9.8E-1:33:25:0:1:153:123\n+chr1\t65299551\t.\tG\tGAATT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:579:557:435:122:21.75%:9.8E-1:36:36:183:252:47:75\n+chr1\t65301238\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:408:386:130:256:66.32%:9.8E-1:37:35:23:107:41:215\n+chr1\t65310489\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:754:714:553:161:22.55%:9.8E-1:35:35:287:266:98:63\n+chr1\t65311214\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:788:738:275:463:62.74%:9.8E-1:35:24:129:146:236:227\n+chr1\t65321250\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:808:739:283:456:61.71%:9.8E-1:34:20:140:143:236:220\n+chr1\t65321388\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:542:506:30:476:94.07%:9.8E-1:36:20:4:26:142:334\n+chr1\t65321419\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:471:426:131:294:69.01%:9.8E-1:35:19:27:104:51:243\n+chr1\t65325970\t.\tC\tT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:491:457:40:417:91.25%:9.8E-1:35:36:8:32:82:335\n+chr1\t65330682\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:482:448:141:307:68.53%:9.8E-1:35:21:21:120:41:266\n+chr1\t65335095\t.\tT\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:1022:957:364:593:61.96%:9.8E-1:35:21:147:217:251:342\n+chr1\t85732065\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:319:295:6:289:97.97%:9.8E-1:37:36:5:1:206:83\n+chr1\t85732133\t.\tG\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:434:405:124:281:69.21%:9.8E-1:36:24:82:42:200:81\n+chr1\t85732941\t.\tA\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:479:423:9:414:97.64%:9.8E-1:37:35:2:7:127:287\n+chr1\t85741921\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:239:218:10:208:95.41%:9.8E-1:34:25:8:2:172:36\n+chr1\t85742012\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:484:437:302:135:30.89%:9.8E-1:35:34:175:127:70:65\n+chr1\t85742338\t.\tG\tC\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:260:216:6:210:97.22%:9.8E-1:30:23:1:5:52:158\n+chr1\t110882444\t.\tA\tG\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:247:223:76:147:65.92%:9.8E-1:32:25:39:37:80:67\n+chr1\t110883569\t.\tA\tT\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:635:585:186:399:68.21%:9.8E-1:34:34:100:86:196:203\n+chr1\t114936079\t.\tT\tA\t.\tPASS\t.\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:375:318:257:61:19.18%:9.8E-1:36:17:108:149:38:23\n' 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| b |
| diff -r 000000000000 -r 1363e5d4a8b8 test-data/slice_out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slice_out.vcf Sun Nov 24 17:12:15 2013 -0500 |
| b |
| @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT panc1_ng +chr1 19071752 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:770:715:219:495:69.23%:9.8E-1:35:21:86:133:184:311 +chr1 19071865 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:517:479:174:305:63.54%:9.8E-1:35:34:42:132:91:214 +chr1 19072808 . G A . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:706:657:228:429:65.3%:9.8E-1:36:19:99:129:197:232 +chr1 19072926 . A G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:673:618:183:435:70.39%:9.8E-1:35:24:96:87:187:248 +chr1 19074980 . C T . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:720:676:221:454:67.06%:9.8E-1:35:35:89:132:226:228 +chr1 19075225 . A G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:718:660:190:468:70.91%:9.8E-1:34:34:93:97:231:237 +chr1 19075327 . C A . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:623:588:178:410:69.73%:9.8E-1:36:36:63:115:142:268 +chr1 36752152 . C T . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:845:780:216:564:72.31%:9.8E-1:36:25:103:113:249:315 +chr1 36759426 . A G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:504:465:152:309:66.45%:9.8E-1:36:36:111:41:250:59 +chr1 36762396 . C T . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:468:377:0:377:100%:9.8E-1:0:19:0:0:127:250 +chr1 36770605 . CTT C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:390:310:229:76:23.6%:9.8E-1:29:29:128:101:41:35 +chr1 40361783 . G C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:533:505:33:471:93.27%:9.8E-1:35:24:9:24:206:265 +chr1 40363054 . G C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:677:646:468:178:27.55%:9.8E-1:36:35:193:275:82:96 +chr1 43812075 . G A . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:692:639:16:621:97.18%:9.8E-1:33:20:10:6:343:278 +chr1 43814864 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:182:150:8:142:94.67%:9.8E-1:27:32:8:0:141:1 +chr1 45796269 . G C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:571:534:0:534:100%:9.8E-1:0:24:0:0:111:423 +chr1 45798555 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:754:685:0:685:100%:9.8E-1:0:24:0:0:366:319 +chr1 45805566 . G C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:327:276:0:276:100%:9.8E-1:0:20:0:0:127:149 +chr1 47682017 . T G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:555:470:10:460:97.87%:9.8E-1:35:34:7:3:286:174 +chr1 47683201 . C T . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:708:660:195:465:70.45%:9.8E-1:35:24:83:112:218:247 +chr1 47684677 . T G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:691:636:27:609:95.75%:9.8E-1:36:20:17:10:319:290 +chr1 47685455 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:407:343:0:343:99.71%:9.8E-1:0:23:0:0:46:297 +chr1 47691568 . GCAGA G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:40:35:15:21:56.76%:9.8E-1:33:29:7:8:7:14 +chr1 47717189 . A G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:714:667:201:464:69.57%:9.8E-1:36:21:115:86:242:222 +chr1 47726087 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:625:603:468:135:22.39%:9.8E-1:36:35:264:204:65:70 +chr1 47735280 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:414:381:98:283:74.28%:9.8E-1:35:36:74:24:225:58 +chr1 47767914 . G A . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:560:533:377:156:29.27%:9.8E-1:35:34:222:155:91:65 +chr1 65325970 . C T . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:491:457:40:417:91.25%:9.8E-1:35:36:8:32:82:335 +chr1 65330682 . G A . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:482:448:141:307:68.53%:9.8E-1:35:21:21:120:41:266 +chr1 65335095 . T C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:1022:957:364:593:61.96%:9.8E-1:35:21:147:217:251:342 +chr1 85732065 . A G . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:319:295:6:289:97.97%:9.8E-1:37:36:5:1:206:83 +chr1 85732133 . G A . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:434:405:124:281:69.21%:9.8E-1:36:24:82:42:200:81 +chr1 85732941 . A C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:479:423:9:414:97.64%:9.8E-1:37:35:2:7:127:287 +chr1 85741921 . G C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:239:218:10:208:95.41%:9.8E-1:34:25:8:2:172:36 +chr1 85742012 . G C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:484:437:302:135:30.89%:9.8E-1:35:34:175:127:70:65 +chr1 85742338 . G C . PASS . GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:0:260:216:6:210:97.22%:9.8E-1:30:23:1:5:52:158 |
| b |
| diff -r 000000000000 -r 1363e5d4a8b8 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Nov 24 17:12:15 2013 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="vcftools" version="0.1.11"> + <repository changeset_revision="61f9ddecde82" name="package_vcftools_0_1_11" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r 1363e5d4a8b8 vcftools_slice.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools_slice.xml Sun Nov 24 17:12:15 2013 -0500 |
| b |
| @@ -0,0 +1,50 @@ +<tool id="vcftools_slice" name="Slice VCF" version="0.1"> + <description>to get data from selected regions</description> + + <requirements> + <requirement type="binary">echo</requirement> + <requirement type="package" version="0.1.11">vcftools</requirement> + </requirements> + + <command> + ## Only works if input is sorted. + vcf-sort ${input} > sorted.vcf + + ## As of v0.1.10, the first line of a BED file is assumed to be a header and ignored, + ## so add a dummy header line if necessary. + #set first_line = open( str($regions) ).readline() + #if first_line.startswith( '#' ): + ## Header already exists, so just link. + ; ln -s $regions regions.bed + #else: + ## Add dummy header. + ; echo '#dummy header' | cat - $regions > regions.bed + #end if + + ## Slice VCF. + ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode + </command> + + <inputs> + <param name="input" label="Input dataset" type="data" format="vcf"/> + <param name="regions" label="Regions" type="data" format="bed"/> + </inputs> + + <outputs> + <data name="output" format="vcf" from_work_dir="output.recode.vcf"/> + </outputs> + + <tests> + <test> + <param name="input" value="slice_in.vcf"/> + <param name="regions" value="regions.bed"/> + <output name="output" file="slice_out.vcf"/> + </test> + </tests> + + <help> + Please see the VCFtools `documentation`__ for help and further information. + + .. __: http://vcftools.sourceforge.net/docs.html + </help> +</tool> |