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comparison test-data/vcfflatten-test1.vcf @ 0:38d93ca9c0f0 draft

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author devteam
date Thu, 19 Mar 2015 14:31:30 -0400
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1 ##fileformat=VCFv4.1
2 ##fileDate=20140610
3 ##source=Dan
4 ##reference=file:///galaxy/data/phiX/sam_index/phiX.fa
5 ##filter="AF > .001"
6 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
7 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
9 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
10 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
11 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
12 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB
13 phiX174 1015 . A C 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0,2:0,0.2:A=8,C=2,G=1, 0:0,0:0,0:A=26,G=1,
14 phiX174 1016 . A T 0 . AC=2;AF=0.0555555555556 GT:AC:AF:NC 0:0:0:A=10, 0:2:0.0769230769231:A=24,T=2,
15 phiX174 1038 . A C 0 . AC=2;AF=0.046511627907 GT:AC:AF:NC 0:2:0.153846153846:A=11,C=2, 0:0:0:A=30,
16 phiX174 1045 . T G 0 . AC=2;AF=0.0425531914894 GT:AC:AF:NC 0:0:0:T=15,G=1, 0:2:0.0625:T=30,G=2,
17 phiX174 1048 . C A 0 . AC=2;AF=0.0434782608696 GT:AC:AF:NC 0:2:0.133333333333:A=2,C=13, 0:0:0:C=31,G=1,
18 phiX174 1050 . A C 0 . AC=3;AF=0.0714285714286 GT:AC:AF:NC 0:0:0:A=12, 0:3:0.1:A=27,C=3,
19 phiX174 1051 . T G 0 . AC=2;AF=0.0487804878049 GT:AC:AF:NC 0:2:0.166666666667:C=1,T=10,G=2, 0:0:0:T=29,G=1,
20 phiX174 1054 . T G 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:2:0.153846153846:T=11,G=2, 0:0:0:T=31,G=1,
21 phiX174 1076 . G C 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,G=17, 0:0:0:G=36,
22 phiX174 1080 . G C 0 . AC=2;AF=0.0344827586207 GT:AC:AF:NC 0:2:0.105263157895:A=1,C=2,T=1,G=17, 0:0:0:C=1,G=39,
23 phiX174 1092 . T G 0 . AC=2;AF=0.0263157894737 GT:AC:AF:NC 0:2:0.0833333333333:C=1,T=22,G=2, 0:0:0:T=52,G=1,
24 phiX174 1093 . T G 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.08:T=23,G=2, 0:0:0:T=52,
25 phiX174 1102 . T C 0 . AC=6;AF=0.0779220779221 GT:AC:AF:NC 0:2:0.0869565217391:C=2,T=21, 0:4:0.0740740740741:C=4,T=50,
26 phiX174 1107 . T G 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:0:0:T=22,G=1, 0:2:0.04:T=48,G=2,
27 phiX174 1110 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.125:C=2,T=14, 0:0:0:C=1,T=56,G=1,
28 phiX174 1121 . T G 0 . AC=3;AF=0.041095890411 GT:AC:AF:NC 0:0:0:T=19, 0:3:0.0555555555556:T=51,G=3,
29 phiX174 1124 . T C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0,2:0,0.117647058824:C=2,T=15,G=1, 0:0,0:0,0:T=48,G=1,
30 phiX174 1125 . T G 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.176470588235:T=14,G=3, 0:0:0:T=49,G=1,
31 phiX174 1131 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0952380952381:T=19,G=2, 0:0:0:T=57,
32 phiX174 1141 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=20,G=1, 0:2:0.0338983050847:T=57,G=2,
33 phiX174 1145 . G C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.0952380952381:C=2,G=19, 0:0:0:G=52,
34 phiX174 1147 . T C 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:2:0.0952380952381:C=2,T=19, 0:0:0:T=50,
35 phiX174 1149 . T C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2,2:0.1,0.1:C=2,T=16,G=2, 0:0,0:0,0:T=54,
36 phiX174 1156 . T G 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:0:0:C=1,T=15, 0:2:0.0416666666667:T=46,G=2,
37 phiX174 1159 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:2,0:0.111111111111,0:C=2,T=16, 0:0,2:0,0.0408163265306:C=1,T=47,G=2,
38 phiX174 1164 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:0:0:C=1,T=16,G=1, 0:4:0.0909090909091:T=40,G=4,
39 phiX174 1168 . T G 0 . AC=4;AF=0.0666666666667 GT:AC:AF:NC 0:2:0.0952380952381:C=1,T=19,G=2, 0:2:0.0512820512821:T=37,G=2,
40 phiX174 1171 . T G 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:T=21,G=2, 0:0:0:T=38,G=1,
41 phiX174 1174 . C A 0 . AC=2;AF=0.0327868852459 GT:AC:AF:NC 0:2:0.0869565217391:A=2,C=21, 0:0:0:A=1,C=38,
42 phiX174 1178 . G C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0740740740741:C=2,T=1,G=25, 0:0:0:G=38,
43 phiX174 1187 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0882352941176:C=1,T=31,G=3, 0:0:0:T=41,
44 phiX174 1189 . T C 0 . AC=3;AF=0.0379746835443 GT:AC:AF:NC 0:3:0.0857142857143:C=3,T=32,G=1, 0:0:0:T=44,
45 phiX174 1200 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:3:0.0882352941176:T=31,G=3, 0:0:0:T=48,G=1,
46 phiX174 1202 . T G 0 . AC=3;AF=0.0365853658537 GT:AC:AF:NC 0:0:0:T=32, 0:3:0.06:T=47,G=3,
47 phiX174 1205 . A C 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=47,C=1,G=1,
48 phiX174 1207 . T G 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:A=1,T=34, 0:2:0.0425531914894:T=45,G=2,
49 phiX174 1214 . G A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:T=1,G=34, 0:2:0.0425531914894:A=2,G=45,
50 phiX174 1216 . C A 0 . AC=2;AF=0.0246913580247 GT:AC:AF:NC 0:0:0:C=34, 0:2:0.0425531914894:A=2,C=45,
51 phiX174 1217 . C A 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0588235294118:A=2,C=32, 0:0:0:C=46,
52 phiX174 1219 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:0:0:C=1,T=33,G=1, 0:2:0.0444444444444:T=43,G=2,
53 phiX174 1223 . C T 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.0555555555556:C=34,T=2, 0:0:0:C=44,
54 phiX174 1227 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0588235294118:A=32,C=2, 0:0:0:A=40,
55 phiX174 1232 . T G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:T=34, 0:2:0.0606060606061:C=1,T=31,G=2,
56 phiX174 1236 . G T 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0606060606061:A=1,T=2,G=31, 0:0:0:G=35,
57 phiX174 1237 . T G 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=1,T=33,G=2, 0:0:0:T=33,G=1,
58 phiX174 1240 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:0,0:0,0:A=32,T=1, 0:0,2:0,0.0555555555556:A=34,C=2,T=1,
59 phiX174 1245 . G T 0 . AC=4;AF=0.0625 GT:AC:AF:NC 0:2:0.0666666666667:C=1,T=2,G=28, 0:2:0.0588235294118:T=2,G=32,
60 phiX174 1247 . A T 0 . AC=2;AF=0.031746031746 GT:AC:AF:NC 0:2:0.0714285714286:A=26,C=1,T=2,G=1, 0:0:0:A=35,
61 phiX174 1250 . A C 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:2:0.0769230769231:A=24,C=2, 0:0:0:A=39,
62 phiX174 1251 . A G 0 . AC=3;AF=0.044776119403 GT:AC:AF:NC 0:0:0:A=29, 0:3:0.0789473684211:A=35,C=1,G=3,
63 phiX174 1253 . T G 0 . AC=4;AF=0.0526315789474 GT:AC:AF:NC 0:2:0.0645161290323:T=29,G=2, 0:2:0.0444444444444:T=43,G=2,
64 phiX174 1257 . T G 0 . AC=2;AF=0.0281690140845 GT:AC:AF:NC 0:0:0:T=26, 0:2:0.0444444444444:T=43,G=2,
65 phiX174 1259 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=28,T=1, 0:2:0.0444444444444:A=43,C=2,G=1,
66 phiX174 1274 . G C 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.0512820512821:C=2,G=37, 0:0:0:G=44,
67 phiX174 1277 . A C 0 . AC=2;AF=0.025 GT:AC:AF:NC 0:2:0.05:A=38,C=2, 0:0:0:A=40,G=1,
68 phiX174 1279 . T G 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0:0:T=39,G=1, 0:2:0.05:C=1,T=38,G=2,
69 phiX174 1284 . T G 0 . AC=3;AF=0.038961038961 GT:AC:AF:NC 0:3,2:0.075,0.05:C=2,T=35,G=3, 0:0,0:0,0:A=1,T=37,
70 phiX174 1289 . A C 0 . AC=3;AF=0.0454545454545 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=28,G=1,
71 phiX174 1296 . A C 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:0:0:A=38, 0:2:0.0769230769231:A=24,C=2,
72 phiX174 1298 . A C 0 . AC=3;AF=0.0491803278689 GT:AC:AF:NC 0:3,0:0.0810810810811,0:A=34,C=3,G=1, 0:0,0:0,0:A=24,C=1,T=1,G=1,
73 phiX174 1306 . T G 0 . AC=5;AF=0.0943396226415 GT:AC:AF:NC 0:5:0.178571428571:T=23,G=5, 0:0:0:C=1,T=25,
74 phiX174 1307 . T G 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.107142857143:T=25,G=3, 0:0:0:C=1,T=27,
75 phiX174 1314 . A G 0 . AC=5;AF=0.0877192982456 GT:AC:AF:NC 0:2,0:0.0740740740741,0:A=25,C=1,G=2, 0:3,0:0.1,0:A=27,C=1,G=3,
76 phiX174 1317 . A C 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0740740740741:A=25,C=2, 0:0:0:A=35,
77 phiX174 1320 . C G 0 . AC=2;AF=0.0322580645161 GT:AC:AF:NC 0:2:0.0769230769231:C=24,G=2, 0:0:0:C=36,
78 phiX174 1322 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.107142857143:C=3,G=25, 0:0:0:G=40,
79 phiX174 1323 . C G 0 . AC=2;AF=0.0298507462687 GT:AC:AF:NC 0:0:0:C=28, 0:2:0.0512820512821:C=37,T=1,G=2,
80 phiX174 1329 . T C 0 . AC=2;AF=0.0277777777778 GT:AC:AF:NC 0:2:0.0666666666667:C=2,T=28, 0:0:0:T=42,G=1,
81 phiX174 1335 . C A 0 . AC=2;AF=0.025974025974 GT:AC:AF:NC 0:2:0.0625:A=2,C=30, 0:0:0:C=45,
82 phiX174 1338 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:T=32, 0:2:0.047619047619:A=2,T=40,
83 phiX174 1345 . T C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:0,0:0,0:T=36,G=1, 0:0,2:0,0.046511627907:C=2,T=41,G=1,
84 phiX174 1347 . A C 0 . AC=2;AF=0.0243902439024 GT:AC:AF:NC 0:2:0.0512820512821:A=37,C=2,G=1, 0:0:0:A=43,
85 phiX174 1348 . T G 0 . AC=2;AF=0.0240963855422 GT:AC:AF:NC 0:2:0.05:T=38,G=2, 0:0:0:T=43,
86 phiX174 1352 . A T 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:0:0:A=34,G=1, 0:2:0.0512820512821:A=37,T=2,
87 phiX174 1354 . T A 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2,0:0.0526315789474,0:T=36,G=2, 0:0,2:0,0.0555555555556:A=2,T=34,G=1,
88 phiX174 1359 . T G 0 . AC=3;AF=0.0405405405405 GT:AC:AF:NC 0:3:0.0714285714286:T=39,G=3, 0:0:0:T=32,G=1,
89 phiX174 1366 . G C 0 . AC=3;AF=0.0428571428571 GT:AC:AF:NC 0:3:0.0714285714286:C=3,T=1,G=39, 0:0:0:G=28,
90 phiX174 1370 . T G 0 . AC=2;AF=0.0289855072464 GT:AC:AF:NC 0:0:0:C=1,T=45,G=1, 0:2:0.0833333333333:A=1,T=22,G=2,
91 phiX174 1373 . T G 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:2:0.0408163265306:T=47,G=2, 0:0:0:T=25,
92 phiX174 1380 . G C 0 . AC=2;AF=0.0238095238095 GT:AC:AF:NC 0:0,2:0,0.0384615384615:C=2,T=1,G=50, 0:0,0:0,0:T=1,G=32,
93 phiX174 1381 . T G 0 . AC=3;AF=0.0361445783133 GT:AC:AF:NC 0:3:0.0576923076923:A=1,T=49,G=3, 0:0:0:T=31,
94 phiX174 1384 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:T=29,G=1,
95 phiX174 1385 . T G 0 . AC=4;AF=0.0512820512821 GT:AC:AF:NC 0:4:0.0816326530612:T=45,G=4, 0:0:0:C=1,T=29,
96 phiX174 1391 . A C 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0408163265306:A=47,C=2, 0:0:0:A=30,C=1,
97 phiX174 1393 . C A 0 . AC=2;AF=0.0253164556962 GT:AC:AF:NC 0:2:0.0425531914894:A=2,C=45, 0:0:0:C=32,
98 phiX174 1396 . T G 0 . AC=3;AF=0.04 GT:AC:AF:NC 0:3:0.0697674418605:T=40,G=3, 0:0:0:T=32,
99 phiX174 1397 . A C 0 . AC=2;AF=0.027027027027 GT:AC:AF:NC 0:0:0:A=42,T=1, 0:2:0.0625:A=30,C=2,
100 phiX174 1400 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2,G=1, 0:0:0:A=31,
101 phiX174 1401 . A C 0 . AC=2;AF=0.027397260274 GT:AC:AF:NC 0:2:0.047619047619:A=40,C=2, 0:0:0:A=31,
102 phiX174 1434 . C T 0 . AC=2;AF=0.0571428571429 GT:AC:AF:NC 0:2:0.142857142857:C=12,T=2, 0:0:0:C=21,
103 phiX174 1438 . G C 0 . AC=2;AF=0.0526315789474 GT:AC:AF:NC 0:0:0:G=15, 0:2:0.0869565217391:C=2,G=21,
104 phiX174 1450 . T G 0 . AC=3;AF=0.0789473684211 GT:AC:AF:NC 0:3:0.176470588235:A=1,C=1,T=14,G=3, 0:0:0:T=21,G=1,
105 phiX174 1459 . T G 0 . AC=3;AF=0.075 GT:AC:AF:NC 0:3:0.142857142857:C=1,T=18,G=3, 0:0:0:T=19,
106 phiX174 1470 . C A 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:0:0:C=29, 0:2:0.0869565217391:A=2,C=21,
107 phiX174 1484 . C G 0 . AC=2;AF=0.0384615384615 GT:AC:AF:NC 0:2:0.0740740740741:A=1,C=25,G=2, 0:0:0:C=25,
108 phiX174 1487 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0689655172414:T=27,G=2, 0:0:0:T=26,
109 phiX174 1491 . G T 0 . AC=2;AF=0.037037037037 GT:AC:AF:NC 0:0:0:T=1,G=26, 0:2:0.0714285714286:T=2,G=26,
110 phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2,
111 phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1,
112 phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28,
113 phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28,
114 phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2,
115 phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32,
116 phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34,
117 phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1,
118 phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3,
119 phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1,
120 phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1,
121 phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45,