Expunge step by step non reliable loci from an initial map.
The squeeze command is invoked either as:
CarthaGene version 1.2-LKH, Copyright (c) 1997-2010 (INRA). CarthaGene comes with ABSOLUTELY NO WARRANTY. CarthaGene is free software. You are welcome to redistribute it, under certain conditions. See the License file for information. Type 'help' for help. # 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 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 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 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 2018-03-23