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Expunge step by step non reliable loci from an initial map.
The squeeze command is invoked either as:
# load two datasets and find markers which appear in linkage groups
# of size greater than 4 in the two datasets
CG> set mrkselection [multigroup 4 {0.5 0.5} {6 6} {Data/panelRH1.id Data/p...
Linkage Groups :
---------------:
LOD threshold=6.00
Distance threshold=50.00:
Group ID : Marker ID List ...
1 : 151
2 : 125
3 : 93
4 : 15
5 : 4 36 60 73 79 104 118 123 138 150 161 160 159 158 157 156 155 1...
6 : 1 10 3 2
Linkage Groups :
---------------:
LOD threshold=6.00
Distance threshold=50.00:
Group ID : Marker ID List ...
1 : 151
2 : 149
3 : 123
4 : 122 129 130 131 127 128 126 125 124 137 140 145 146 144 143 142...
5 : 121
6 : 119 120
7 : 118
8 : 116
9 : 115 117
10 : 110 114 113 112 111
11 : 102
12 : 93
13 : 80 81 85 92 100 106 103 105 104 101 99 97 96 95 94 91 98 90 89 ...
14 : 79
15 : 74 78 77 76 75
16 : 73
17 : 59 63 69 72 71 68 67 66 65 64 62 61 60 70
18 : 58
19 : 46 55 57 56 54 53 52 51 50 49 48 47
20 : 41 45 44 43 42
21 : 40
22 : 35 36 37 39 38
23 : 30 31
24 : 11 15 20 28 33 32 29 24 27 26 25 23 22 21 19 18 17 14 16 13 12 34
25 : 10
26 : 4 9 8 7 6 5
27 : 1 3 2
122 129 130 131 127 128 126 124 137 140 145 146 144 143 142 141 139 138 136...
CG>
# merge the two panels
CG> dsmergor 1 2
{3 merged by order 161 273}
CG>
# set the current selection of markers
CG> mrkselset $mrkselection
CG>
# remove double markers
CG> mrkdouble
Possible double markers:
4 = 5 [45.9]
CG> mrkmerges
Markers 4 and 5 merged in 4.
CG>
# find a good map
CG> lkhn 1 -1
[-2693.73]
Best map with log10-likelihood = -2693.73
TSP: optimum= 2612.586000 lowerbound= 2610.091410 gap= 0.095575% totaltime=...
Map -1 : log10-likelihood = -2693.73
-------:
Set : Marker List ...
1 : 9 8 7 6 4 11 13 12 14 17 16 18 19 20 21 22 23 24 27 25 26 28 29 32 3...
2 : 9 8 7 6 4 11 13 12 14 17 16 18 19 20 21 22 23 24 27 25 26 28 29 32 3...
CG>
# remove dubious markers
CG> squeeze {50 60} {lkhn 1 -1}
Those loci have been removed : 122 37 105 114 98
The best map is now :
Map 0 : log10-likelihood = -2561.26
-------:
Set : Marker List ...
1 : 9 8 7 6 4 11 13 12 14 17 16 18 19 20 21 22 23 24 27 25 26 28 29 32 3...
2 : 9 8 7 6 4 11 13 12 14 17 16 18 19 20 21 22 23 24 27 25 26 28 29 32 3...
CG> bestprintd
Map 0 : log10-likelihood = -2561.26, log-e-likelihood = -5897.52
-------:
Data Set Number 1 :
Markers Distance Cumulative Theta 2pt
Pos Id name (%%age) LOD
1 9 9 19.0 cR 0.0 cR 17.3 %% 14.9
2 8 8 0.0 cR 19.0 cR 0.0 %% 18.6
3 7 7 24.4 cR 19.0 cR 21.7 %% 12.1
4 6 6 20.4 cR 43.5 cR 18.4 %% 10.0
5 5 5 0.0 cR 63.8 cR 0.0 %% ------
5 4 4 19.8 cR 63.8 cR 18.0 %% 12.3
6 11 11 21.1 cR 83.6 cR 19.1 %% 12.0
7 13 13 17.4 cR 104.8 cR 16.0 %% 10.6
8 12 12 19.1 cR 122.2 cR 17.4 %% 7.5
9 14 14 35.1 cR 141.2 cR 29.6 %% 5.7
10 17 17 3.8 cR 176.3 cR 3.8 %% 15.9
11 16 16 0.0 cR 180.2 cR 0.0 %% 19.3
12 18 18 3.5 cR 180.2 cR 3.4 %% 15.9
13 19 19 0.0 cR 183.6 cR 0.0 %% 17.0
14 20 20 7.0 cR 183.6 cR 6.7 %% 14.6
15 21 21 7.0 cR 190.6 cR 6.7 %% 15.3
16 22 22 8.6 cR 197.6 cR 8.3 %% 13.2
17 23 23 4.4 cR 206.2 cR 4.3 %% 13.7
18 24 24 13.5 cR 210.6 cR 12.6 %% 10.7
19 27 27 11.0 cR 224.1 cR 10.4 %% 12.2
20 25 25 7.1 cR 235.1 cR 6.9 %% 14.7
21 26 26 15.2 cR 242.2 cR 14.1 %% 11.3
22 28 28 7.3 cR 257.4 cR 7.0 %% 14.4
23 29 29 0.0 cR 264.7 cR 0.0 %% 17.0
24 32 32 3.5 cR 264.7 cR 3.4 %% 16.7
25 33 33 3.5 cR 268.1 cR 3.4 %% 16.7
26 34 34 29.8 cR 271.6 cR 25.7 %% 7.2
27 35 35 25.3 cR 301.4 cR 22.3 %% 7.7
28 36 36 19.3 cR 326.6 cR 17.5 %% 9.7
29 38 38 30.4 cR 345.9 cR 26.2 %% 5.4
30 39 39 33.2 cR 376.3 cR 28.2 %% 3.0
31 44 44 45.1 cR 409.5 cR 36.3 %% 3.7
32 41 41 26.1 cR 454.6 cR 23.0 %% 10.1
33 42 42 6.8 cR 480.7 cR 6.6 %% 15.9
34 43 43 3.3 cR 487.6 cR 3.3 %% 17.9
35 45 45 7.8 cR 490.9 cR 7.5 %% 15.1
36 46 46 16.3 cR 498.7 cR 15.0 %% 12.4
37 49 49 10.1 cR 515.0 cR 9.6 %% 13.3
38 51 51 3.2 cR 525.1 cR 3.2 %% 17.8
39 50 50 0.0 cR 528.3 cR 0.0 %% 21.7
40 47 47 0.0 cR 528.3 cR 0.0 %% 21.7
41 48 48 0.0 cR 528.3 cR 0.0 %% 21.7
42 52 52 0.0 cR 528.3 cR 0.0 %% 21.0
43 53 53 3.2 cR 528.3 cR 3.2 %% 17.1
44 54 54 6.4 cR 531.5 cR 6.2 %% 15.7
45 55 55 37.9 cR 538.0 cR 31.5 %% 7.6
46 56 56 12.2 cR 575.9 cR 11.5 %% 10.6
47 57 57 39.2 cR 588.0 cR 32.5 %% 7.7
48 59 59 51.6 cR 627.3 cR 40.3 %% 6.6
49 60 60 12.5 cR 678.8 cR 11.7 %% 12.0
50 64 64 29.1 cR 691.3 cR 25.2 %% 8.8
51 63 63 22.6 cR 720.4 cR 20.3 %% 12.7
52 61 61 5.9 cR 743.0 cR 5.7 %% 19.4
53 62 62 11.0 cR 748.9 cR 10.4 %% 14.8
54 65 65 13.5 cR 759.9 cR 12.6 %% 13.1
55 66 66 22.7 cR 773.4 cR 20.3 %% 11.5
56 69 69 10.7 cR 796.2 cR 10.1 %% 14.2
57 71 71 6.5 cR 806.8 cR 6.3 %% 15.4
58 72 72 16.4 cR 813.3 cR 15.1 %% 15.5
59 70 70 3.6 cR 829.6 cR 3.5 %% 19.9
60 68 68 37.3 cR 833.2 cR 31.1 %% 6.3
61 67 67 46.2 cR 870.5 cR 37.0 %% 4.1
62 77 77 37.8 cR 916.6 cR 31.5 %% 7.7
63 75 75 0.0 cR 954.4 cR 0.0 %% 22.1
64 76 76 6.1 cR 954.4 cR 5.9 %% 18.5
65 78 78 16.4 cR 960.5 cR 15.1 %% 14.4
66 74 74 43.3 cR 976.9 cR 35.1 %% 8.1
67 80 80 35.8 cR 1020.2 cR 30.1 %% 7.7
68 81 81 14.0 cR 1056.1 cR 13.0 %% 12.4
69 82 82 3.1 cR 1070.0 cR 3.1 %% 19.6
70 83 83 29.4 cR 1073.2 cR 25.5 %% 9.4
71 84 84 19.9 cR 1102.6 cR 18.0 %% 10.9
72 85 85 17.4 cR 1122.5 cR 15.9 %% 12.9
73 86 86 10.5 cR 1139.8 cR 10.0 %% 17.3
74 88 88 35.8 cR 1150.3 cR 30.1 %% 8.7
75 87 87 18.7 cR 1186.1 cR 17.1 %% 9.0
76 89 89 21.8 cR 1204.8 cR 19.6 %% 9.6
77 90 90 37.3 cR 1226.6 cR 31.1 %% 9.2
78 91 91 3.4 cR 1263.9 cR 3.4 %% 19.8
79 92 92 27.3 cR 1267.3 cR 23.9 %% 10.7
80 94 94 29.4 cR 1294.6 cR 25.5 %% 9.6
81 95 95 0.0 cR 1324.0 cR 0.0 %% 19.0
82 96 96 20.7 cR 1324.1 cR 18.7 %% 13.3
83 97 97 9.4 cR 1344.7 cR 8.9 %% 17.4
84 99 99 0.0 cR 1354.1 cR 0.0 %% 21.5
85 100 100 3.1 cR 1354.1 cR 3.0 %% 18.9
86 101 101 24.3 cR 1357.2 cR 21.6 %% 11.7
87 104 104 10.1 cR 1381.5 cR 9.6 %% 14.0
88 103 103 20.6 cR 1391.6 cR 18.6 %% 9.5
89 106 106 7.6 cR 1412.3 cR 7.3 %% 15.1
90 107 107 3.2 cR 1419.8 cR 3.1 %% 19.1
91 109 109 0.0 cR 1423.0 cR 0.0 %% 21.7
92 108 108 0.0 cR 1423.0 cR 0.0 %% 21.7
93 111 111 3.2 cR 1423.1 cR 3.1 %% 19.1
94 113 113 10.1 cR 1426.2 cR 9.6 %% 14.0
95 112 112 6.6 cR 1436.4 cR 6.4 %% 15.8
96 110 110 76.2 cR 1442.9 cR 53.3 %% 3.9
97 124 124 24.9 cR 1519.1 cR 22.1 %% 9.6
98 126 126 18.3 cR 1544.1 cR 16.7 %% 8.9
99 127 127 49.8 cR 1562.4 cR 39.2 %% 4.1
100 129 129 18.8 cR 1612.1 cR 17.1 %% 8.9
101 128 128 24.9 cR 1630.9 cR 22.1 %% 7.3
102 130 130 11.1 cR 1655.8 cR 10.5 %% 9.8
103 131 131 36.0 cR 1666.9 cR 30.2 %% 6.5
104 134 134 14.2 cR 1702.9 cR 13.3 %% 12.4
105 133 133 16.9 cR 1717.2 cR 15.5 %% 8.1
106 136 136 25.2 cR 1734.0 cR 22.3 %% 7.5
107 138 138 16.7 cR 1759.2 cR 15.4 %% 12.9
108 141 141 5.0 cR 1775.9 cR 4.9 %% 15.5
109 139 139 12.3 cR 1780.9 cR 11.6 %% 13.9
110 140 140 0.0 cR 1793.2 cR 0.0 %% 22.7
111 142 142 0.0 cR 1793.2 cR 0.0 %% 22.7
112 135 135 0.0 cR 1793.2 cR 0.0 %% 22.7
113 137 137 3.1 cR 1793.2 cR 3.0 %% 20.1
114 132 132 33.1 cR 1796.3 cR 28.2 %% 10.7
115 143 143 8.6 cR 1829.4 cR 8.2 %% 19.2
116 145 145 2.9 cR 1838.0 cR 2.8 %% 20.7
117 144 144 11.9 cR 1840.9 cR 11.2 %% 16.3
118 146 146 6.4 cR 1852.8 cR 6.2 %% 19.7
119 148 148 22.6 cR 1859.2 cR 20.2 %% 13.3
120 152 152 16.6 cR 1881.8 cR 15.3 %% 12.6
121 154 154 9.4 cR 1898.3 cR 9.0 %% 15.7
122 159 159 14.1 cR 1907.8 cR 13.2 %% 16.9
123 160 160 0.0 cR 1921.9 cR 0.0 %% 26.5
124 161 161 13.9 cR 1921.9 cR 13.0 %% 16.8
125 157 157 8.4 cR 1935.8 cR 8.1 %% 18.7
126 158 158 8.3 cR 1944.3 cR 8.0 %% 19.1
127 155 155 14.2 cR 1952.6 cR 13.3 %% 16.9
128 156 156 14.6 cR 1966.8 cR 13.5 %% 17.1
129 153 153 12.9 cR 1981.4 cR 12.1 %% 16.7
130 150 150 18.1 cR 1994.2 cR 16.6 %% 13.5
131 147 147 ---------
2012.3 cR
131 markers, log10-likelihood = -836.64
log-e-likelihood = -1926.44
retention proba. = 0.21
Data Set Number 2 :
Markers Distance Cumulative Theta 2pt
Pos Id name (%%age) LOD
1 9 9 29.5 cR 0.0 cR 25.6 %% 9.0
2 8 8 9.0 cR 29.5 cR 8.6 %% 14.0
3 7 7 24.6 cR 38.6 cR 21.8 %% 11.3
4 6 6 8.1 cR 63.1 cR 7.8 %% 18.9
5 5 5 0.0 cR 71.3 cR 0.0 %% ------
5 4 4 80.6 cR 71.3 cR 55.3 %% 2.7
6 11 11 24.6 cR 151.9 cR 21.8 %% 10.4
7 13 13 10.9 cR 176.5 cR 10.3 %% 17.0
8 12 12 37.8 cR 187.4 cR 31.5 %% 6.3
9 14 14 28.7 cR 225.2 cR 24.9 %% 9.0
10 17 17 11.8 cR 253.9 cR 11.1 %% 20.5
11 16 16 8.4 cR 265.6 cR 8.0 %% 23.3
12 18 18 15.6 cR 274.0 cR 14.4 %% 18.7
13 19 19 10.3 cR 289.6 cR 9.8 %% 20.6
14 20 20 4.8 cR 299.9 cR 4.7 %% 25.3
15 21 21 25.9 cR 304.7 cR 22.8 %% 13.9
16 22 22 0.0 cR 330.6 cR 0.0 %% 22.3
17 23 23 15.3 cR 330.6 cR 14.2 %% 12.3
18 24 24 15.3 cR 345.9 cR 14.2 %% 12.4
19 27 27 14.3 cR 361.3 cR 13.3 %% 15.3
20 25 25 2.6 cR 375.6 cR 2.6 %% 20.4
21 26 26 16.6 cR 378.2 cR 15.3 %% 14.4
22 28 28 40.3 cR 394.8 cR 33.2 %% 7.6
23 29 29 17.8 cR 435.1 cR 16.3 %% 11.3
24 32 32 32.8 cR 452.9 cR 28.0 %% 9.8
25 33 33 14.7 cR 485.7 cR 13.7 %% 17.0
26 34 34 55.8 cR 500.4 cR 42.8 %% 7.2
27 35 35 26.2 cR 556.2 cR 23.0 %% 11.3
28 36 36 22.9 cR 582.4 cR 20.4 %% 9.6
29 38 38 18.0 cR 605.3 cR 16.4 %% 9.2
30 39 39 97.6 cR 623.2 cR 62.3 %% 0.4
31 44 44 26.1 cR 720.9 cR 23.0 %% 9.4
32 41 41 5.2 cR 747.0 cR 5.1 %% 21.0
33 42 42 2.5 cR 752.2 cR 2.5 %% 23.3
34 43 43 5.2 cR 754.7 cR 5.1 %% 21.0
35 45 45 54.3 cR 759.9 cR 41.9 %% 7.2
36 46 46 15.4 cR 814.2 cR 14.2 %% 22.1
37 49 49 15.1 cR 829.6 cR 14.0 %% 22.8
38 51 51 12.2 cR 844.7 cR 11.5 %% 21.1
39 50 50 7.3 cR 856.9 cR 7.0 %% 22.4
40 47 47 9.9 cR 864.1 cR 9.5 %% 20.5
41 48 48 30.6 cR 874.1 cR 26.3 %% 9.3
42 52 52 35.1 cR 904.6 cR 29.6 %% 8.4
43 53 53 14.0 cR 939.8 cR 13.1 %% 19.5
44 54 54 22.1 cR 953.8 cR 19.8 %% 19.8
45 55 55 42.1 cR 975.9 cR 34.4 %% 13.9
46 56 56 2.3 cR 1018.0 cR 2.3 %% 30.6
47 57 57 62.1 cR 1020.4 cR 46.2 %% 10.0
48 59 59 34.5 cR 1082.4 cR 29.2 %% 15.8
49 60 60 25.5 cR 1117.0 cR 22.5 %% 14.0
50 64 64 25.5 cR 1142.5 cR 22.5 %% 14.0
51 63 63 15.5 cR 1168.1 cR 14.4 %% 24.0
52 61 61 2.8 cR 1183.6 cR 2.8 %% 31.4
53 62 62 27.4 cR 1186.4 cR 24.0 %% 17.1
54 65 65 16.6 cR 1213.8 cR 15.3 %% 21.5
55 66 66 30.0 cR 1230.4 cR 26.0 %% 16.4
56 69 69 9.4 cR 1260.5 cR 9.0 %% 24.5
57 71 71 40.7 cR 1269.9 cR 33.4 %% 10.3
58 72 72 46.3 cR 1310.5 cR 37.1 %% 5.4
59 70 70 36.8 cR 1356.9 cR 30.8 %% 7.6
60 68 68 13.4 cR 1393.6 cR 12.6 %% 17.9
61 67 67 93.5 cR 1407.0 cR 60.7 %% 3.4
62 77 77 18.6 cR 1500.5 cR 17.0 %% 17.1
63 75 75 17.7 cR 1519.2 cR 16.2 %% 16.2
64 76 76 13.7 cR 1536.9 cR 12.8 %% 19.5
65 78 78 16.0 cR 1550.6 cR 14.8 %% 18.5
66 74 74 81.7 cR 1566.6 cR 55.8 %% 5.7
67 80 80 36.9 cR 1648.3 cR 30.8 %% 11.7
68 81 81 19.2 cR 1685.1 cR 17.4 %% 16.9
69 82 82 19.1 cR 1704.3 cR 17.4 %% 19.2
70 83 83 33.4 cR 1723.4 cR 28.4 %% 14.5
71 84 84 25.9 cR 1756.7 cR 22.8 %% 18.3
72 85 85 23.5 cR 1782.6 cR 20.9 %% 19.1
73 86 86 9.5 cR 1806.1 cR 9.1 %% 23.8
74 88 88 17.7 cR 1815.7 cR 16.2 %% 16.1
75 87 87 31.2 cR 1833.4 cR 26.8 %% 7.9
76 89 89 9.4 cR 1864.6 cR 9.0 %% 12.7
77 90 90 20.1 cR 1874.0 cR 18.2 %% 16.1
78 91 91 7.6 cR 1894.1 cR 7.3 %% 25.5
79 92 92 11.8 cR 1901.7 cR 11.1 %% 23.4
80 94 94 6.9 cR 1913.5 cR 6.7 %% 26.4
81 95 95 24.9 cR 1920.4 cR 22.0 %% 17.8
82 96 96 28.6 cR 1945.2 cR 24.9 %% 15.8
83 97 97 48.0 cR 1973.8 cR 38.1 %% 10.9
84 99 99 9.6 cR 2021.8 cR 9.1 %% 25.2
85 100 100 6.4 cR 2031.3 cR 6.2 %% 29.6
86 101 101 17.2 cR 2037.7 cR 15.8 %% 24.1
87 104 104 18.0 cR 2054.9 cR 16.5 %% 22.6
88 103 103 42.3 cR 2072.9 cR 34.5 %% 11.3
89 106 106 22.3 cR 2115.2 cR 20.0 %% 18.4
90 107 107 21.9 cR 2137.5 cR 19.7 %% 22.1
91 109 109 49.4 cR 2159.4 cR 39.0 %% 10.5
92 108 108 61.2 cR 2208.8 cR 45.8 %% 5.4
93 111 111 12.2 cR 2270.0 cR 11.4 %% 22.8
94 113 113 0.0 cR 2282.2 cR 0.0 %% 34.4
95 112 112 13.0 cR 2282.2 cR 12.2 %% 25.8
96 110 110 106.3 cR 2295.2 cR 65.4 %% 4.6
97 124 124 7.7 cR 2401.5 cR 7.4 %% 31.1
98 126 126 2.8 cR 2409.1 cR 2.8 %% 33.4
99 127 127 23.5 cR 2412.0 cR 20.9 %% 19.0
100 129 129 11.6 cR 2435.4 cR 11.0 %% 21.8
101 128 128 8.4 cR 2447.0 cR 8.1 %% 23.8
102 130 130 46.4 cR 2455.5 cR 37.2 %% 11.5
103 131 131 12.7 cR 2501.9 cR 11.9 %% 19.5
104 134 134 14.6 cR 2514.6 cR 13.6 %% 16.9
105 133 133 60.2 cR 2529.2 cR 45.2 %% 5.0
106 136 136 39.5 cR 2589.4 cR 32.6 %% 9.5
107 138 138 19.7 cR 2628.9 cR 17.9 %% 15.3
108 141 141 28.2 cR 2648.6 cR 24.6 %% 13.9
109 139 139 4.7 cR 2676.8 cR 4.5 %% 29.8
110 140 140 17.3 cR 2681.5 cR 15.9 %% 20.7
111 142 142 36.6 cR 2698.8 cR 30.6 %% 14.2
112 135 135 17.3 cR 2735.4 cR 15.9 %% 22.8
113 137 137 21.5 cR 2752.7 cR 19.4 %% 22.7
114 132 132 42.0 cR 2774.2 cR 34.3 %% 15.8
115 143 143 25.7 cR 2816.2 cR 22.7 %% 22.1
116 145 145 6.7 cR 2841.9 cR 6.4 %% 30.8
117 144 144 36.1 cR 2848.6 cR 30.3 %% 17.1
118 146 146 31.2 cR 2884.6 cR 26.8 %% 17.4
119 148 148 30.0 cR 2915.8 cR 26.0 %% 14.9
120 152 152 28.8 cR 2945.9 cR 25.0 %% 16.2
121 154 154 29.0 cR 2974.7 cR 25.2 %% 17.6
122 159 159 8.5 cR 3003.7 cR 8.2 %% 28.7
123 160 160 23.3 cR 3012.2 cR 20.8 %% 22.5
124 161 161 32.3 cR 3035.5 cR 27.6 %% 17.9
125 157 157 16.2 cR 3067.7 cR 14.9 %% 22.0
126 158 158 10.8 cR 3083.9 cR 10.3 %% 26.1
127 155 155 15.2 cR 3094.8 cR 14.1 %% 24.1
128 156 156 14.5 cR 3110.0 cR 13.5 %% 25.9
129 153 153 20.8 cR 3124.5 cR 18.8 %% 23.8
130 150 150 87.0 cR 3145.3 cR 58.1 %% 7.1
131 147 147 ---------
3232.3 cR
131 markers, log10-likelihood = -1724.62
log-e-likelihood = -3971.08
retention proba. = 0.15
0
Thomas Schiex 2009-10-27