# HG changeset patch
# User devteam
# Date 1385331237 18000
# Node ID 23436d1d0fa1d27d6d97508ffd002c632122833f

Uploaded

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
@@ -0,0 +1,108 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
+chr1	2491205	.	C	T	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:SDP:PVAL:RD:ADR:RBQ:AD	.	0/1:397:0:22:31.91%:89:82:188:445:9.8E-1:270:38:34:127
+chr1	2985808	.	T	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:88:0:17:3.19%:0:64:21:9.8E-1:333:85:3:30:3
+chr1	2985812	.	C	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:158:0:23:6.33%:0:129:19:9.8E-1:328:148:10:29:10
+chr1	2985885	.	C	G	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:64:0:20:25%:0:48:0:9.8E-1:70:48:16:34:16	0/1:60:0:20:26.67%:0:44:0:9.8E-1:62:44:16:34:16
+chr1	3301721	.	C	T	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:619:0:24:66.77%:279:75:130:9.8E-1:687:205:135:35:414	1/1:609:0:24:90.31%:382:21:38:9.8E-1:658:59:168:35:550
+chr1	3327904	.	G	A	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:762:0:24:30.84%:121:241:286:9.8E-1:815:527:114:35:235
+chr1	3328180	.	A	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:380:0:21:1.05%:0:204:172:9.8E-1:497:376:4:31:4
+chr1	3328358	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:278:0:25:100%:131:0:0:9.8E-1:314:0:147:0:278	1/1:307:0:25:100%:158:0:0:9.8E-1:348:0:149:0:307
+chr1	3328659	.	C	T	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:362:0:19:18.78%:35:184:110:9.8E-1:417:294:33:35:68	.
+chr1	3328755	.	T	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:280:0:20:1.07%:3:152:125:9.8E-1:346:277:0:29:3
+chr1	3329369	.	T	A	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:183:0:27:1.09%:1:121:60:9.8E-1:201:181:1:33:2
+chr1	3329384	.	C	T	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:147:0:26:19.05%:6:87:32:9.8E-1:161:119:22:33:28	.
+chr1	3342109	.	G	T	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:330:0:22:56.06%:119:38:106:9.8E-1:433:144:66:32:185
+chr1	3342844	.	T	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:197:0:20:1.02%:1:167:28:9.8E-1:226:195:1:34:2
+chr1	3350409	.	G	A	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:471:0:25:66.67%:180:82:75:9.8E-1:567:157:134:33:314	0/1:525:0:25:4%:7:235:269:9.8E-1:612:504:14:33:21
+chr1	3351625	.	A	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:226:0:21:1.77%:0:81:141:9.8E-1:299:222:4:30:4
+chr1	3352161	.	T	TA	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:467:0:33:22.29%:59:195:167:9.8E-1:511:362:46:34:105	.
+chr1	3352227	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:447:0:32:99.78%:256:1:0:9.8E-1:645:1:190:26:446	1/1:524:0:34:99.81%:293:0:0:9.8E-1:605:0:230:0:523
+chr1	3352347	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:427:0:34:100%:126:0:0:9.8E-1:517:0:301:0:427	1/1:404:0:35:99.75%:133:0:0:9.8E-1:495:0:270:0:403
+chr1	3352502	.	CG	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:337:0:25:1.18%:2:146:188:9.8E-1:405:334:2:20:4
+chr1	3352503	.	G	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:304:0:19:100%:170:0:0:9.8E-1:449:0:133:0:303	1/1:276:0:20:100%:144:0:0:9.8E-1:407:0:129:0:273
+chr1	3352541	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:401:0:25:100%:189:0:0:9.8E-1:466:0:212:0:401	1/1:383:0:25:99.74%:192:0:0:9.8E-1:433:0:190:0:382
+chr1	3352579	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:482:0:24:100%:231:0:0:9.8E-1:533:0:251:0:482	1/1:463:0:25:100%:226:0:0:9.8E-1:515:0:237:0:463
+chr1	3352763	.	CT	C	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:369:0:31:29.32%:62:105:143:9.8E-1:437:248:50:33:112	0/1:391:0:31:71.8%:176:50:43:9.8E-1:450:93:127:33:303
+chr1	3352784	.	A	G	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:357:0:25:29.05%:54:93:160:9.8E-1:443:253:50:30:104	1/1:392:0:25:99.49%:231:1:1:9.8E-1:448:2:159:32:390
+chr1	3352872	.	A	C	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:471:0:22:29.3%:104:86:247:9.8E-1:590:333:34:33:138	0/1:468:0:22:35.68%:101:74:227:9.8E-1:597:301:66:33:167
+chr1	3353531	.	A	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:349:0:17:1.15%:0:125:220:9.8E-1:444:345:4:32:4
+chr1	3353890	.	A	G	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:430:0:34:99.77%:242:0:0:9.8E-1:478:0:187:0:429	1/1:423:0:35:100%:227:0:0:9.8E-1:471:0:196:0:423
+chr1	3353949	.	A	G	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:621:0:22:99.84%:421:0:0:9.8E-1:690:0:199:0:620	1/1:585:0:22:99.83%:390:1:0:9.8E-1:641:1:194:40:584
+chr1	3354595	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:461:0:19:99.35%:197:3:0:9.8E-1:519:3:261:30:458	1/1:483:0:19:100%:230:0:0:9.8E-1:545:0:253:0:483
+chr1	3354615	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:459:0:19:100%:220:0:0:9.8E-1:495:0:239:0:459	1/1:459:0:19:99.56%:235:0:0:9.8E-1:499:0:222:0:457
+chr1	3355136	.	A	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:612:0:24:58.01%:116:163:93:9.8E-1:638:256:239:37:355
+chr1	18957546	.	G	A	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:275:0:24:58.18%:36:91:24:9.8E-1:299:115:124:36:160
+chr1	18957678	.	G	T	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:82:0:23:2.44%:1:57:23:9.8E-1:89:80:1:32:2
+chr1	18960722	.	G	C	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:648:0:22:24.54%:121:143:346:9.8E-1:701:489:38:34:159	0/1:599:0:22:28.55%:131:117:311:9.8E-1:645:428:40:35:171
+chr1	19027239	.	A	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:421:0:33:58.29%:155:67:108:9.8E-1:479:175:91:30:246
+chr1	19029546	.	A	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:329:0:22:56.97%:114:55:85:9.8E-1:367:140:74:33:188
+chr1	19071752	.	T	C	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:715:0:21:69.23%:184:133:86:9.8E-1:770:219:311:35:495	1/1:710:0:22:93.24%:277:31:17:9.8E-1:768:48:385:32:662
+chr1	19071865	.	T	C	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:479:0:34:63.54%:91:132:42:9.8E-1:517:174:214:35:305	0/1:531:0:33:2.82%:4:349:167:9.8E-1:561:516:11:34:15
+chr1	19072808	.	G	A	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:657:0:19:65.3%:197:129:99:9.8E-1:706:228:232:36:429	0/1:696:0:20:1.72%:3:388:295:9.8E-1:720:683:9:36:12
+chr1	19072926	.	A	G	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:618:0:24:70.39%:187:87:96:9.8E-1:673:183:248:35:435	1/1:588:0:24:96.77%:278:10:9:9.8E-1:648:19:291:33:569
+chr1	19074980	.	C	T	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:676:0:35:67.06%:226:132:89:9.8E-1:720:221:228:35:454	0/1:674:0:35:1.34%:4:355:309:9.8E-1:697:664:5:35:9
+chr1	19075225	.	A	G	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:660:0:34:70.91%:231:97:93:9.8E-1:718:190:237:34:468	1/1:664:0:35:97.59%:303:10:6:9.8E-1:726:16:345:31:648
+chr1	19075327	.	C	A	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:588:0:36:69.73%:142:115:63:9.8E-1:623:178:268:36:410	0/1:594:0:37:1.35%:4:377:209:9.8E-1:611:586:4:36:8
+chr1	28931625	.	T	G	.	PASS	AC=2;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	1/1:847:0:36:94.45%:375:24:23:9.8E-1:909:47:425:34:800
+chr1	28939918	.	T	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:507:0:24:1.18%:6:457:44:9.8E-1:662:501:0:36:6
+chr1	36752152	.	C	T	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:780:0:25:72.31%:249:113:103:9.8E-1:845:216:315:36:564	0/1:726:0:24:34.57%:107:279:196:9.8E-1:761:475:144:36:251
+chr1	36759426	.	A	G	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:465:0:36:66.45%:250:41:111:9.8E-1:504:152:59:36:309	0/1:492:0:32:1.22%:5:121:365:9.8E-1:502:486:1:36:6
+chr1	36762396	.	C	T	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:377:0:19:100%:127:0:0:9.8E-1:468:0:250:0:377	1/1:430:0:19:99.77%:140:0:0:9.8E-1:516:0:289:0:429
+chr1	36770047	.	C	CT	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:309:0:24:9.67%:13:109:149:9.8E-1:395:258:19:32:32
+chr1	36770605	.	CTT	CT,C	.	PASS	AC=1,1;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/2:310:0:29:23.6%:41:101:128:9.8E-1:390:229:35:29:76	0/1:336:0:28:4.41%:10:139:177:9.8E-1:423:316:5:29:15
+chr1	40361307	.	TA	T	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:441:0:32:5.2%:13:177:241:9.8E-1:481:418:10:33:23
+chr1	40361783	.	G	C	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:505:0:24:93.27%:206:24:9:9.8E-1:533:33:265:35:471	0/1:560:0:24:2.32%:5:321:225:9.8E-1:577:546:8:36:13
+chr1	40362066	.	C	A	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:596:0:24:31.21%:105:179:231:9.8E-1:638:410:81:36:186
+chr1	40363054	.	G	C	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:646:0:35:27.55%:82:275:193:9.8E-1:677:468:96:36:178	1/1:619:0:35:97.25%:265:11:6:9.8E-1:659:17:337:35:602
+chr1	43812075	.	G	A	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:639:0:20:97.18%:343:6:10:9.8E-1:692:16:278:33:621	0/1:636:0:20:65.41%:223:94:124:9.8E-1:668:218:193:35:416
+chr1	43814864	.	T	C	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:150:0:32:94.67%:141:0:8:9.8E-1:182:8:1:27:142	0/1:149:0:32:59.06%:87:2:57:9.8E-1:188:59:1:26:88
+chr1	43814891	.	T	TC	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:195:0:22:2.55%:5:13:178:9.8E-1:260:191:0:30:5
+chr1	43814893	.	C	CG	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:182:0:16:1.63%:3:17:163:9.8E-1:263:180:0:32:3
+chr1	43814902	.	T	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:132:0:18:2.27%:3:24:105:9.8E-1:300:129:0:28:3
+chr1	45796269	.	G	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:534:0:24:100%:111:0:0:9.8E-1:571:0:423:0:534	1/1:489:0:24:99.59%:85:0:0:9.8E-1:524:0:403:0:488
+chr1	45797505	.	C	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:286:0:35:37.76%:46:103:75:9.8E-1:320:178:62:34:108
+chr1	45798555	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:685:0:24:100%:366:0:0:9.8E-1:754:0:319:0:685	1/1:677:0:24:100%:389:0:0:9.8E-1:739:0:288:0:677
+chr1	45799209	.	A	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:287:0:21:1.05%:0:177:105:9.8E-1:389:282:3:30:3
+chr1	45805566	.	G	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:276:0:20:100%:127:0:0:9.8E-1:327:0:149:0:276	1/1:269:0:20:100%:137:0:0:9.8E-1:323:0:132:0:269
+chr1	45805617	.	T	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:183:0:15:1.09%:0:98:83:9.8E-1:263:181:2:29:2
+chr1	47682017	.	T	G	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:470:0:34:97.87%:286:3:7:9.8E-1:555:10:174:35:460	1/1:522:0:34:99.23%:320:3:1:9.8E-1:579:4:198:31:518
+chr1	47683201	.	C	T	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:660:0:24:70.45%:218:112:83:9.8E-1:708:195:247:35:465	0/1:653:0:25:1.07%:2:360:286:9.8E-1:678:646:5:36:7
+chr1	47683464	.	G	A	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:643:0:25:3.11%:14:302:321:9.8E-1:677:623:6:36:20
+chr1	47683607	.	G	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:645:0:36:2.79%:11:322:305:9.8E-1:672:627:7:35:18
+chr1	47684677	.	T	G	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:636:0:20:95.75%:319:10:17:9.8E-1:691:27:290:36:609	1/1:587:0:19:94.89%:250:14:16:9.8E-1:642:30:307:34:557
+chr1	47685455	.	T	C	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:343:0:23:99.71%:46:0:0:9.8E-1:407:0:297:0:343	1/1:333:0:22:99.7%:40:1:0:9.8E-1:395:1:292:35:332
+chr1	47691568	.	GCAGA	G	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:35:0:29:56.76%:7:8:7:9.8E-1:40:15:14:33:21	1/1:26:0:27:78.57%:11:4:1:9.8E-1:29:5:11:35:22
+chr1	47717189	.	A	G	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:667:0:21:69.57%:242:86:115:9.8E-1:714:201:222:36:464	1/1:621:0:21:98.07%:338:6:6:9.8E-1:677:12:271:37:609
+chr1	47726087	.	T	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:603:0:35:22.39%:65:204:264:9.8E-1:625:468:70:36:135	.
+chr1	47735280	.	T	C	.	PASS	AC=3;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:381:0:36:74.28%:225:24:74:9.8E-1:414:98:58:35:283	1/1:430:0:36:99.07%:336:0:4:9.8E-1:458:4:90:35:426
+chr1	47735328	.	T	G	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:477:0:18:1.47%:7:220:250:9.8E-1:635:470:0:32:7
+chr1	47746678	.	G	C	.	PASS	AC=1;AN=2;SF=1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	.	0/1:774:0:24:3.62%:16:385:360:9.8E-1:803:745:12:36:28
+chr1	47767914	.	G	A	.	PASS	AC=2;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:533:0:34:29.27%:91:155:222:9.8E-1:560:377:65:35:156	0/1:529:0:32:3.4%:7:231:280:9.8E-1:544:511:11:35:18
+chr1	51433821	.	G	GC	.	PASS	AC=4;AN=4;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:407:0:32:89.34%:88:32:12:9.8E-1:454:44:306:33:394	1/1:426:0:32:91.74%:86:20:16:9.8E-1:461:36:325:32:411
+chr1	51433863	.	G	GC	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:318:0:31:92.96%:70:20:3:9.8E-1:373:23:247:33:317	.
+chr1	51433888	.	A	AG	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:284:0:29:87.77%:85:31:3:9.8E-1:343:34:202:33:287	.
+chr1	51822188	.	GA	G	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:277:0:30:10.25%:18:62:164:9.8E-1:406:226:11:34:29	.
+chr1	51873951	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:740:0:37:29.59%:88:332:189:9.8E-1:773:521:131:37:219	.
+chr1	59248813	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:412:0:33:100%:80:0:0:9.8E-1:463:0:332:0:412	.
+chr1	59249031	.	T	G	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:249:0:22:100%:103:0:0:9.8E-1:284:0:146:0:249	.
+chr1	59249347	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:278:0:25:99.28%:153:1:0:9.8E-1:320:1:123:33:276	.
+chr1	65299551	.	G	GAATT	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:557:0:36:21.75%:47:252:183:9.8E-1:579:435:75:36:122	.
+chr1	65301238	.	A	G	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:386:0:35:66.32%:41:107:23:9.8E-1:408:130:215:37:256	.
+chr1	65310489	.	T	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:714:0:35:22.55%:98:266:287:9.8E-1:754:553:63:35:161	.
+chr1	65311214	.	G	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:738:0:24:62.74%:236:146:129:9.8E-1:788:275:227:35:463	.
+chr1	65321250	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:739:0:20:61.71%:236:143:140:9.8E-1:808:283:220:34:456	.
+chr1	65321388	.	G	A	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:506:0:20:94.07%:142:26:4:9.8E-1:542:30:334:36:476	.
+chr1	65321419	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:426:0:19:69.01%:51:104:27:9.8E-1:471:131:243:35:294	.
+chr1	65325970	.	C	T	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:457:0:36:91.25%:82:32:8:9.8E-1:491:40:335:35:417	.
+chr1	65330682	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:448:0:21:68.53%:41:120:21:9.8E-1:482:141:266:35:307	.
+chr1	65335095	.	T	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:957:0:21:61.96%:251:217:147:9.8E-1:1022:364:342:35:593	.
+chr1	85732065	.	A	G	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:295:0:36:97.97%:206:1:5:9.8E-1:319:6:83:37:289	.
+chr1	85732133	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:405:0:24:69.21%:200:42:82:9.8E-1:434:124:81:36:281	.
+chr1	85732941	.	A	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:423:0:35:97.64%:127:7:2:9.8E-1:479:9:287:37:414	.
+chr1	85741921	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:218:0:25:95.41%:172:2:8:9.8E-1:239:10:36:34:208	.
+chr1	85742012	.	G	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:437:0:34:30.89%:70:127:175:9.8E-1:484:302:65:35:135	.
+chr1	85742338	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:216:0:23:97.22%:52:5:1:9.8E-1:260:6:158:30:210	.
+chr1	110882444	.	A	G	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:223:0:25:65.92%:80:37:39:9.8E-1:247:76:67:32:147	.
+chr1	110883569	.	A	T	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:585:0:34:68.21%:196:86:100:9.8E-1:635:186:203:34:399	.
+chr1	114936079	.	T	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:318:0:17:19.18%:38:149:108:9.8E-1:375:257:23:36:61	.
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
@@ -0,0 +1,77 @@
+##fileformat=VCFv4.1
+##source_20131021.2=vcf-subset(r797) -a -e -c sample1 input.vcf.sorted.gz
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1
+chr1	2985885	.	C	G	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:64:0:20:25%:0:48:0:9.8E-1:70:48:16:34:16
+chr1	3301721	.	C	T	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:619:0:24:66.77%:279:75:130:9.8E-1:687:205:135:35:414
+chr1	3328358	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:278:0:25:100%:131:0:0:9.8E-1:314:0:147:0:278
+chr1	3328659	.	C	T	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:362:0:19:18.78%:35:184:110:9.8E-1:417:294:33:35:68
+chr1	3329384	.	C	T	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:147:0:26:19.05%:6:87:32:9.8E-1:161:119:22:33:28
+chr1	3350409	.	G	A	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:471:0:25:66.67%:180:82:75:9.8E-1:567:157:134:33:314
+chr1	3352161	.	T	TA	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:467:0:33:22.29%:59:195:167:9.8E-1:511:362:46:34:105
+chr1	3352227	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:447:0:32:99.78%:256:1:0:9.8E-1:645:1:190:26:446
+chr1	3352347	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:427:0:34:100%:126:0:0:9.8E-1:517:0:301:0:427
+chr1	3352503	.	G	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:304:0:19:100%:170:0:0:9.8E-1:449:0:133:0:303
+chr1	3352541	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:401:0:25:100%:189:0:0:9.8E-1:466:0:212:0:401
+chr1	3352579	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:482:0:24:100%:231:0:0:9.8E-1:533:0:251:0:482
+chr1	3352763	.	CT	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:369:0:31:29.32%:62:105:143:9.8E-1:437:248:50:33:112
+chr1	3352784	.	A	G	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:357:0:25:29.05%:54:93:160:9.8E-1:443:253:50:30:104
+chr1	3352872	.	A	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:471:0:22:29.3%:104:86:247:9.8E-1:590:333:34:33:138
+chr1	3353890	.	A	G	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:430:0:34:99.77%:242:0:0:9.8E-1:478:0:187:0:429
+chr1	3353949	.	A	G	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:621:0:22:99.84%:421:0:0:9.8E-1:690:0:199:0:620
+chr1	3354595	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:461:0:19:99.35%:197:3:0:9.8E-1:519:3:261:30:458
+chr1	3354615	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:459:0:19:100%:220:0:0:9.8E-1:495:0:239:0:459
+chr1	18960722	.	G	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:648:0:22:24.54%:121:143:346:9.8E-1:701:489:38:34:159
+chr1	19071752	.	T	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:715:0:21:69.23%:184:133:86:9.8E-1:770:219:311:35:495
+chr1	19071865	.	T	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:479:0:34:63.54%:91:132:42:9.8E-1:517:174:214:35:305
+chr1	19072808	.	G	A	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:657:0:19:65.3%:197:129:99:9.8E-1:706:228:232:36:429
+chr1	19072926	.	A	G	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:618:0:24:70.39%:187:87:96:9.8E-1:673:183:248:35:435
+chr1	19074980	.	C	T	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:676:0:35:67.06%:226:132:89:9.8E-1:720:221:228:35:454
+chr1	19075225	.	A	G	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:660:0:34:70.91%:231:97:93:9.8E-1:718:190:237:34:468
+chr1	19075327	.	C	A	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:588:0:36:69.73%:142:115:63:9.8E-1:623:178:268:36:410
+chr1	36752152	.	C	T	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:780:0:25:72.31%:249:113:103:9.8E-1:845:216:315:36:564
+chr1	36759426	.	A	G	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:465:0:36:66.45%:250:41:111:9.8E-1:504:152:59:36:309
+chr1	36762396	.	C	T	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:377:0:19:100%:127:0:0:9.8E-1:468:0:250:0:377
+chr1	36770605	.	CTT	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:310:0:29:23.6%:41:101:128:9.8E-1:390:229:35:29:76
+chr1	40361783	.	G	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:505:0:24:93.27%:206:24:9:9.8E-1:533:33:265:35:471
+chr1	40363054	.	G	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:646:0:35:27.55%:82:275:193:9.8E-1:677:468:96:36:178
+chr1	43812075	.	G	A	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:639:0:20:97.18%:343:6:10:9.8E-1:692:16:278:33:621
+chr1	43814864	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:150:0:32:94.67%:141:0:8:9.8E-1:182:8:1:27:142
+chr1	45796269	.	G	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:534:0:24:100%:111:0:0:9.8E-1:571:0:423:0:534
+chr1	45798555	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:685:0:24:100%:366:0:0:9.8E-1:754:0:319:0:685
+chr1	45805566	.	G	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:276:0:20:100%:127:0:0:9.8E-1:327:0:149:0:276
+chr1	47682017	.	T	G	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:470:0:34:97.87%:286:3:7:9.8E-1:555:10:174:35:460
+chr1	47683201	.	C	T	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:660:0:24:70.45%:218:112:83:9.8E-1:708:195:247:35:465
+chr1	47684677	.	T	G	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:636:0:20:95.75%:319:10:17:9.8E-1:691:27:290:36:609
+chr1	47685455	.	T	C	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:343:0:23:99.71%:46:0:0:9.8E-1:407:0:297:0:343
+chr1	47691568	.	GCAGA	G	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:35:0:29:56.76%:7:8:7:9.8E-1:40:15:14:33:21
+chr1	47717189	.	A	G	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:667:0:21:69.57%:242:86:115:9.8E-1:714:201:222:36:464
+chr1	47726087	.	T	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:603:0:35:22.39%:65:204:264:9.8E-1:625:468:70:36:135
+chr1	47735280	.	T	C	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:381:0:36:74.28%:225:24:74:9.8E-1:414:98:58:35:283
+chr1	47767914	.	G	A	.	PASS	AC=1;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:533:0:34:29.27%:91:155:222:9.8E-1:560:377:65:35:156
+chr1	51433821	.	G	GC	.	PASS	AC=2;AN=2;SF=0,1	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:407:0:32:89.34%:88:32:12:9.8E-1:454:44:306:33:394
+chr1	51433863	.	G	GC	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:318:0:31:92.96%:70:20:3:9.8E-1:373:23:247:33:317
+chr1	51433888	.	A	AG	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:284:0:29:87.77%:85:31:3:9.8E-1:343:34:202:33:287
+chr1	51822188	.	GA	G	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:277:0:30:10.25%:18:62:164:9.8E-1:406:226:11:34:29
+chr1	51873951	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:740:0:37:29.59%:88:332:189:9.8E-1:773:521:131:37:219
+chr1	59248813	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:412:0:33:100%:80:0:0:9.8E-1:463:0:332:0:412
+chr1	59249031	.	T	G	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:249:0:22:100%:103:0:0:9.8E-1:284:0:146:0:249
+chr1	59249347	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:278:0:25:99.28%:153:1:0:9.8E-1:320:1:123:33:276
+chr1	65299551	.	G	GAATT	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:557:0:36:21.75%:47:252:183:9.8E-1:579:435:75:36:122
+chr1	65301238	.	A	G	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:386:0:35:66.32%:41:107:23:9.8E-1:408:130:215:37:256
+chr1	65310489	.	T	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:714:0:35:22.55%:98:266:287:9.8E-1:754:553:63:35:161
+chr1	65311214	.	G	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:738:0:24:62.74%:236:146:129:9.8E-1:788:275:227:35:463
+chr1	65321250	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:739:0:20:61.71%:236:143:140:9.8E-1:808:283:220:34:456
+chr1	65321388	.	G	A	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:506:0:20:94.07%:142:26:4:9.8E-1:542:30:334:36:476
+chr1	65321419	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:426:0:19:69.01%:51:104:27:9.8E-1:471:131:243:35:294
+chr1	65325970	.	C	T	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:457:0:36:91.25%:82:32:8:9.8E-1:491:40:335:35:417
+chr1	65330682	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:448:0:21:68.53%:41:120:21:9.8E-1:482:141:266:35:307
+chr1	65335095	.	T	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:957:0:21:61.96%:251:217:147:9.8E-1:1022:364:342:35:593
+chr1	85732065	.	A	G	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:295:0:36:97.97%:206:1:5:9.8E-1:319:6:83:37:289
+chr1	85732133	.	G	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:405:0:24:69.21%:200:42:82:9.8E-1:434:124:81:36:281
+chr1	85732941	.	A	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:423:0:35:97.64%:127:7:2:9.8E-1:479:9:287:37:414
+chr1	85741921	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:218:0:25:95.41%:172:2:8:9.8E-1:239:10:36:34:208
+chr1	85742012	.	G	C	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:437:0:34:30.89%:70:127:175:9.8E-1:484:302:65:35:135
+chr1	85742338	.	G	C	.	PASS	AC=2;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	1/1:216:0:23:97.22%:52:5:1:9.8E-1:260:6:158:30:210
+chr1	110882444	.	A	G	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:223:0:25:65.92%:80:37:39:9.8E-1:247:76:67:32:147
+chr1	110883569	.	A	T	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:585:0:34:68.21%:196:86:100:9.8E-1:635:186:203:34:399
+chr1	114936079	.	T	A	.	PASS	AC=1;AN=2;SF=0	GT:DP:GQ:ABQ:FREQ:ADF:RDR:RDF:PVAL:SDP:RD:ADR:RBQ:AD	0/1:318:0:17:19.18%:38:149:108:9.8E-1:375:257:23:36:61
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
@@ -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>
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
@@ -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>