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author devteam
date Sun, 24 Nov 2013 17:13:57 -0500
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##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