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Commit message:
Uploaded |
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added:
test-data/subset_in.vcf test-data/subset_out.vcf tool_dependencies.xml vcftools_subset.xml |
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| diff -r 000000000000 -r 23436d1d0fa1 test-data/subset_in.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_in.vcf Sun Nov 24 17:13:57 2013 -0500 |
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| b'@@ -0,0 +1,108 @@\n+##fileformat=VCFv4.1\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\tsample2\n+chr1\t2491205\t.\tC\tT\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:SDP:PVAL:RD:ADR:RBQ:AD\t.\t0/1:397:0:22:31.91%:89:82:188:445:9.8E-1:270:38:34:127\n+chr1\t2985808\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:88:0:17:3.19%:0:64:21:9.8E-1:333:85:3:30:3\n+chr1\t2985812\t.\tC\tG\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:158:0:23:6.33%:0:129:19:9.8E-1:328:148:10:29:10\n+chr1\t2985885\t.\tC\tG\t.\tPASS\tAC=2;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:64:0:20:25%:0:48:0:9.8E-1:70:48:16:34:16\t0/1:60:0:20:26.67%:0:44:0:9.8E-1:62:44:16:34:16\n+chr1\t3301721\t.\tC\tT\t.\tPASS\tAC=3;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:619:0:24:66.77%:279:75:130:9.8E-1:687:205:135:35:414\t1/1:609:0:24:90.31%:382:21:38:9.8E-1:658:59:168:35:550\n+chr1\t3327904\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:762:0:24:30.84%:121:241:286:9.8E-1:815:527:114:35:235\n+chr1\t3328180\t.\tA\tC\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:380:0:21:1.05%:0:204:172:9.8E-1:497:376:4:31:4\n+chr1\t3328358\t.\tT\tC\t.\tPASS\tAC=4;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:278:0:25:100%:131:0:0:9.8E-1:314:0:147:0:278\t1/1:307:0:25:100%:158:0:0:9.8E-1:348:0:149:0:307\n+chr1\t3328659\t.\tC\tT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:362:0:19:18.78%:35:184:110:9.8E-1:417:294:33:35:68\t.\n+chr1\t3328755\t.\tT\tG\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:280:0:20:1.07%:3:152:125:9.8E-1:346:277:0:29:3\n+chr1\t3329369\t.\tT\tA\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:183:0:27:1.09%:1:121:60:9.8E-1:201:181:1:33:2\n+chr1\t3329384\t.\tC\tT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:147:0:26:19.05%:6:87:32:9.8E-1:161:119:22:33:28\t.\n+chr1\t3342109\t.\tG\tT\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:330:0:22:56.06%:119:38:106:9.8E-1:433:144:66:32:185\n+chr1\t3342844\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:197:0:20:1.02%:1:167:28:9.8E-1:226:195:1:34:2\n+chr1\t3350409\t.\tG\tA\t.\tPASS\tAC=2;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:471:0:25:66.67%:180:82:75:9.8E-1:567:157:134:33:314\t0/1:525:0:25:4%:7:235:269:9.8E-1:612:504:14:33:21\n+chr1\t3351625\t.\tA\tC\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:226:0:21:1.77%:0:81:141:9.8E-1:299:222:4:30:4\n+chr1\t3352161\t.\tT\tTA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:467:0:33:22.29%:59:195:167:9.8E-1:511:362:46:34:105\t.\n+chr1\t3352227\t.\tT\tC\t.\tPASS\tAC=4;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:447:0:32:99.78%:256:1:0:9.8E-1:645:1:190:26:446\t1/1:524:0:34:99.81%:293:0:0:9.8E-1:605:0:230:0:523\n+chr1\t3352347\t.\tT\tC\t.\tPASS\tAC=4;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:427:0:34:100%:126:0:0:9.8E-1:517:0:301:0:427\t1/1:404:0:35:99.75%:133:0:0:9.8E-1:495:0:270:0:403\n+chr1\t3352502\t.\tCG\tC\t.\tPASS\tAC=1;AN=2;SF=1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t.\t0/1:337:0:25:1.18%:2:146:188:9.8E-1:405:334:2:20:4\n+chr1\t3352503\t.\tG\tC\t.\tPASS\tAC=4;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:304:0:19:100%:170:0:0:9.8E-1:449:0:133:0:303\t1/1:276:0:20:100%:144:0:0:9.8E-1:407:0:129:0:273\n+chr1\t3352541\t.\tT\tC\t.\tPASS\tAC=4;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:401:0:25:100%:189:0:0:9.8E-1:466:0:212:0:401\t1/1:383:0:25:99.74%:192:0:0:9.8E-1:433:0:190:0:382\n+chr1\t3352579\t.\tT\tC\t.\tPASS\tAC=4;AN=4;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:482:0:24:100%:231:0:0:9.8E-1:533:0:251:0:482\t1/1:463:0:25:100%:226:0:0:9.8E-1:515:0:237:0:463\n+chr1\t3352763\t.\tCT\tC\t'..b'20:16:9.8E-1:461:36:325:32:411\n+chr1\t51433863\t.\tG\tGC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:318:0:31:92.96%:70:20:3:9.8E-1:373:23:247:33:317\t.\n+chr1\t51433888\t.\tA\tAG\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:284:0:29:87.77%:85:31:3:9.8E-1:343:34:202:33:287\t.\n+chr1\t51822188\t.\tGA\tG\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:277:0:30:10.25%:18:62:164:9.8E-1:406:226:11:34:29\t.\n+chr1\t51873951\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:740:0:37:29.59%:88:332:189:9.8E-1:773:521:131:37:219\t.\n+chr1\t59248813\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:412:0:33:100%:80:0:0:9.8E-1:463:0:332:0:412\t.\n+chr1\t59249031\t.\tT\tG\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:249:0:22:100%:103:0:0:9.8E-1:284:0:146:0:249\t.\n+chr1\t59249347\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:278:0:25:99.28%:153:1:0:9.8E-1:320:1:123:33:276\t.\n+chr1\t65299551\t.\tG\tGAATT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:557:0:36:21.75%:47:252:183:9.8E-1:579:435:75:36:122\t.\n+chr1\t65301238\t.\tA\tG\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:386:0:35:66.32%:41:107:23:9.8E-1:408:130:215:37:256\t.\n+chr1\t65310489\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:714:0:35:22.55%:98:266:287:9.8E-1:754:553:63:35:161\t.\n+chr1\t65311214\t.\tG\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:738:0:24:62.74%:236:146:129:9.8E-1:788:275:227:35:463\t.\n+chr1\t65321250\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:739:0:20:61.71%:236:143:140:9.8E-1:808:283:220:34:456\t.\n+chr1\t65321388\t.\tG\tA\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:506:0:20:94.07%:142:26:4:9.8E-1:542:30:334:36:476\t.\n+chr1\t65321419\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:426:0:19:69.01%:51:104:27:9.8E-1:471:131:243:35:294\t.\n+chr1\t65325970\t.\tC\tT\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:457:0:36:91.25%:82:32:8:9.8E-1:491:40:335:35:417\t.\n+chr1\t65330682\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:448:0:21:68.53%:41:120:21:9.8E-1:482:141:266:35:307\t.\n+chr1\t65335095\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:957:0:21:61.96%:251:217:147:9.8E-1:1022:364:342:35:593\t.\n+chr1\t85732065\t.\tA\tG\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:295:0:36:97.97%:206:1:5:9.8E-1:319:6:83:37:289\t.\n+chr1\t85732133\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:405:0:24:69.21%:200:42:82:9.8E-1:434:124:81:36:281\t.\n+chr1\t85732941\t.\tA\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:423:0:35:97.64%:127:7:2:9.8E-1:479:9:287:37:414\t.\n+chr1\t85741921\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:218:0:25:95.41%:172:2:8:9.8E-1:239:10:36:34:208\t.\n+chr1\t85742012\t.\tG\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:437:0:34:30.89%:70:127:175:9.8E-1:484:302:65:35:135\t.\n+chr1\t85742338\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:216:0:23:97.22%:52:5:1:9.8E-1:260:6:158:30:210\t.\n+chr1\t110882444\t.\tA\tG\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:223:0:25:65.92%:80:37:39:9.8E-1:247:76:67:32:147\t.\n+chr1\t110883569\t.\tA\tT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:585:0:34:68.21%:196:86:100:9.8E-1:635:186:203:34:399\t.\n+chr1\t114936079\t.\tT\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:318:0:17:19.18%:38:149:108:9.8E-1:375:257:23:36:61\t.\n' 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| diff -r 000000000000 -r 23436d1d0fa1 test-data/subset_out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_out.vcf Sun Nov 24 17:13:57 2013 -0500 |
| b |
| b'@@ -0,0 +1,77 @@\n+##fileformat=VCFv4.1\n+##source_20131021.2=vcf-subset(r797) -a -e -c sample1 input.vcf.sorted.gz\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\n+chr1\t2985885\t.\tC\tG\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:64:0:20:25%:0:48:0:9.8E-1:70:48:16:34:16\n+chr1\t3301721\t.\tC\tT\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:619:0:24:66.77%:279:75:130:9.8E-1:687:205:135:35:414\n+chr1\t3328358\t.\tT\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:278:0:25:100%:131:0:0:9.8E-1:314:0:147:0:278\n+chr1\t3328659\t.\tC\tT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:362:0:19:18.78%:35:184:110:9.8E-1:417:294:33:35:68\n+chr1\t3329384\t.\tC\tT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:147:0:26:19.05%:6:87:32:9.8E-1:161:119:22:33:28\n+chr1\t3350409\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:471:0:25:66.67%:180:82:75:9.8E-1:567:157:134:33:314\n+chr1\t3352161\t.\tT\tTA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:467:0:33:22.29%:59:195:167:9.8E-1:511:362:46:34:105\n+chr1\t3352227\t.\tT\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:447:0:32:99.78%:256:1:0:9.8E-1:645:1:190:26:446\n+chr1\t3352347\t.\tT\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:427:0:34:100%:126:0:0:9.8E-1:517:0:301:0:427\n+chr1\t3352503\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:304:0:19:100%:170:0:0:9.8E-1:449:0:133:0:303\n+chr1\t3352541\t.\tT\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:401:0:25:100%:189:0:0:9.8E-1:466:0:212:0:401\n+chr1\t3352579\t.\tT\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:482:0:24:100%:231:0:0:9.8E-1:533:0:251:0:482\n+chr1\t3352763\t.\tCT\tC\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:369:0:31:29.32%:62:105:143:9.8E-1:437:248:50:33:112\n+chr1\t3352784\t.\tA\tG\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:357:0:25:29.05%:54:93:160:9.8E-1:443:253:50:30:104\n+chr1\t3352872\t.\tA\tC\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:471:0:22:29.3%:104:86:247:9.8E-1:590:333:34:33:138\n+chr1\t3353890\t.\tA\tG\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:430:0:34:99.77%:242:0:0:9.8E-1:478:0:187:0:429\n+chr1\t3353949\t.\tA\tG\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:621:0:22:99.84%:421:0:0:9.8E-1:690:0:199:0:620\n+chr1\t3354595\t.\tT\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:461:0:19:99.35%:197:3:0:9.8E-1:519:3:261:30:458\n+chr1\t3354615\t.\tT\tC\t.\tPASS\tAC=2;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:459:0:19:100%:220:0:0:9.8E-1:495:0:239:0:459\n+chr1\t18960722\t.\tG\tC\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:648:0:22:24.54%:121:143:346:9.8E-1:701:489:38:34:159\n+chr1\t19071752\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:715:0:21:69.23%:184:133:86:9.8E-1:770:219:311:35:495\n+chr1\t19071865\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:479:0:34:63.54%:91:132:42:9.8E-1:517:174:214:35:305\n+chr1\t19072808\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:657:0:19:65.3%:197:129:99:9.8E-1:706:228:232:36:429\n+chr1\t19072926\t.\tA\tG\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:618:0:24:70.39%:187:87:96:9.8E-1:673:183:248:35:435\n+chr1\t19074980\t.\tC\tT\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:676:0:35:67.06%:226:132:89:9.8E-1:720:221:228:35:454\n+chr1\t19075225\t.\tA\tG\t.\tPASS\tAC=1;AN=2;SF=0,1\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PV'..b'R:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:407:0:32:89.34%:88:32:12:9.8E-1:454:44:306:33:394\n+chr1\t51433863\t.\tG\tGC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:318:0:31:92.96%:70:20:3:9.8E-1:373:23:247:33:317\n+chr1\t51433888\t.\tA\tAG\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:284:0:29:87.77%:85:31:3:9.8E-1:343:34:202:33:287\n+chr1\t51822188\t.\tGA\tG\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:277:0:30:10.25%:18:62:164:9.8E-1:406:226:11:34:29\n+chr1\t51873951\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:740:0:37:29.59%:88:332:189:9.8E-1:773:521:131:37:219\n+chr1\t59248813\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:412:0:33:100%:80:0:0:9.8E-1:463:0:332:0:412\n+chr1\t59249031\t.\tT\tG\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:249:0:22:100%:103:0:0:9.8E-1:284:0:146:0:249\n+chr1\t59249347\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:278:0:25:99.28%:153:1:0:9.8E-1:320:1:123:33:276\n+chr1\t65299551\t.\tG\tGAATT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:557:0:36:21.75%:47:252:183:9.8E-1:579:435:75:36:122\n+chr1\t65301238\t.\tA\tG\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:386:0:35:66.32%:41:107:23:9.8E-1:408:130:215:37:256\n+chr1\t65310489\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:714:0:35:22.55%:98:266:287:9.8E-1:754:553:63:35:161\n+chr1\t65311214\t.\tG\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:738:0:24:62.74%:236:146:129:9.8E-1:788:275:227:35:463\n+chr1\t65321250\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:739:0:20:61.71%:236:143:140:9.8E-1:808:283:220:34:456\n+chr1\t65321388\t.\tG\tA\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:506:0:20:94.07%:142:26:4:9.8E-1:542:30:334:36:476\n+chr1\t65321419\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:426:0:19:69.01%:51:104:27:9.8E-1:471:131:243:35:294\n+chr1\t65325970\t.\tC\tT\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:457:0:36:91.25%:82:32:8:9.8E-1:491:40:335:35:417\n+chr1\t65330682\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:448:0:21:68.53%:41:120:21:9.8E-1:482:141:266:35:307\n+chr1\t65335095\t.\tT\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:957:0:21:61.96%:251:217:147:9.8E-1:1022:364:342:35:593\n+chr1\t85732065\t.\tA\tG\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:295:0:36:97.97%:206:1:5:9.8E-1:319:6:83:37:289\n+chr1\t85732133\t.\tG\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:405:0:24:69.21%:200:42:82:9.8E-1:434:124:81:36:281\n+chr1\t85732941\t.\tA\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:423:0:35:97.64%:127:7:2:9.8E-1:479:9:287:37:414\n+chr1\t85741921\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:218:0:25:95.41%:172:2:8:9.8E-1:239:10:36:34:208\n+chr1\t85742012\t.\tG\tC\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:437:0:34:30.89%:70:127:175:9.8E-1:484:302:65:35:135\n+chr1\t85742338\t.\tG\tC\t.\tPASS\tAC=2;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t1/1:216:0:23:97.22%:52:5:1:9.8E-1:260:6:158:30:210\n+chr1\t110882444\t.\tA\tG\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:223:0:25:65.92%:80:37:39:9.8E-1:247:76:67:32:147\n+chr1\t110883569\t.\tA\tT\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:585:0:34:68.21%:196:86:100:9.8E-1:635:186:203:34:399\n+chr1\t114936079\t.\tT\tA\t.\tPASS\tAC=1;AN=2;SF=0\tGT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD\t0/1:318:0:17:19.18%:38:149:108:9.8E-1:375:257:23:36:61\n' |
| b |
| diff -r 000000000000 -r 23436d1d0fa1 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Nov 24 17:13:57 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 23436d1d0fa1 vcftools_subset.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools_subset.xml Sun Nov 24 17:13:57 2013 -0500 |
| b |
| @@ -0,0 +1,63 @@ +<tool id="vcftools_subset" name="Subset" version="0.1"> + <description>columns from a VCF dataset</description> + + <requirements> + <requirement type="package">tabix</requirement> + <requirement type="package" version="0.1.11">vcftools</requirement> + </requirements> + + <command> + ln -s ${input} input.vcf ; + + ## Sort file. + sort -k1,1 -k2,2n input.vcf > input.vcf.sorted ; + + ## Compress. + bgzip input.vcf.sorted ; + + ## Index. + tabix -p vcf input.vcf.sorted.gz ; + + ## Subset. + vcf-subset ${trim_alt_alleles} ${exclude_rows_with_no_variants} -c "${columns}" input.vcf.sorted.gz > $output + </command> + + <inputs> + <param name="input" label="Input dataset" type="data" format="vcf"/> + <param name="columns" label="Columns" type="text" value=""/> + <param name="trim_alt_alleles" type="select" label="Remove alternate alleles if not found in the subset" help=""> + <option value="" selected="True">No</option> + <option value="-a">Yes</option> + </param> + <param name="exclude_rows_with_no_variants" type="select" label="Exclude rows not containing variants" help=""> + <option value="" selected="True">No</option> + <option value="-e">Yes</option> + </param> + </inputs> + + <outputs> + <data name="output" format="vcf"/> + </outputs> + + <stdio> + <regex match=".*" source="both" level="log" description="tool progress"/> + </stdio> + + <tests> + <test> + <param name="input" value="subset_in.vcf"/> + <param name="columns" value="sample1"/> + <param name="trim_alt_alleles" value="Yes"/> + <param name="exclude_rows_with_no_variants" value="Yes"/> + <!-- 2 lines diff because command line with full file path is included in output VCF, and + it not possible to match full file path. --> + <output name="output" file="subset_out.vcf" lines_diff="2"/> + </test> + </tests> + + <help> + Please see the VCFtools `documentation`__ for help and further information. + + .. __: http://vcftools.sourceforge.net/docs.html + </help> +</tool> |