LDhat lookup table
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11 months ago
Matteo ▴ 10

Hi everyone,

I am new to the field and I am trying to understand what is the best way to compute a lookup table for LDhat for 135 individuals (n = 270). I see that there are pre-computed lookup tables that I can use but none of them gets close to my n value (https://github.com/auton1/LDhat/tree/master/lk_files). Alternatively, I could use this lookup table for n = 320 (https://zenodo.org/record/3934350). Should I use the second lookup table because it has an "n" similar to my data or is there is something else I should consider to make this decision (such as the t value: e.g. n192_t0.001 vs n320_t0.01?). Thank you in advance!

Matteo

LDhat • 444 views
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Hi!

Did you manage to fix this?

I run convert successfully on 60 unphased diploid samples (1500bp), hence I used lktable available in LDhat repository for 120 haplotypes, butwhen running interval with the following command:

LDhat/interval -seq Pantro6.CM009241.2.consens_60s.sites.txt -loc Pantro6.CM009241.2.consens_60s.locs.txt -lk lk_n120_t0.001.gz

I still get this error message:

Analysing 60 genotypes of length 3731 seg sites  
Reading sequences in fasta format.  
Sequence :  1 CM009241.2_PD_0257: T:  300 C:  175 A: 3222 G:    0 -:   34   
Sequence :  2 CM009241.2_PD_0258: T:  298 C:  177 A: 3232 G:    0 -:   24   
Sequence :  3 CM009241.2_PD_0427: T:  282 C:  178 A: 3207 G:    0 -:   64   
Sequence :  4 CM009241.2_SAMEA4374763: T:  291 C:  166 A: 3209 G:    0 -:   65  
Sequence :  5 CM009241.2_SAMEA4374764: T:  283 C:  172 A: 3204 G:    0 -:   72    
Sequence :  6 CM009241.2_SAMEA4374765: T:  259 C:  163 A: 3187 G:    0 -:  122    
Sequence :  7 CM009241.2_SAMEA4374766: T:  278 C:  165 A: 3176 G:    0 -:  112    
Sequence :  8 CM009241.2_SAMEA4374767: T:  272 C:  170 A: 3182 G:    0 -:  107       
Sequence :  9 CM009241.2_SAMEA4374768: T:  239 C:  171 A: 3150 G:    0 -:  171    
Sequence : 10 CM009241.2_SAMEA4374769: T:  245 C:  165 A: 3140 G:    0 -:  181    
Sequence : 11 CM009241.2_SAMEA4374770: T:  290 C:  160 A: 3171 G:    0 -:  110    
Sequence : 12 CM009241.2_SAMEA4374771: T:  249 C:  154 A: 3140 G:    0 -:  188    
Sequence : 13 CM009241.2_SAMEA4374772: T:  269 C:  165 A: 3205 G:    0 -:   92    
Sequence : 14 CM009241.2_SAMEA4374773: T:  278 C:  158 A: 3194 G:    0 -:  101    
Sequence : 15 CM009241.2_SAMEA4374774: T:  295 C:  160 A: 3227 G:    0 -:   49    
Sequence : 16 CM009241.2_SAMEA4374775: T:  297 C:  166 A: 3195 G:    0 -:   73    
Sequence : 17 CM009241.2_SAMEA4374776: T:  302 C:  163 A: 3226 G:    0 -:   40    
Sequence : 18 CM009241.2_SAMEA4374777: T:  304 C:  167 A: 3233 G:    0 -:   27    
Sequence : 19 CM009241.2_SAMEA4374778: T:  314 C:  164 A: 3228 G:    0 -:   25    
Sequence : 20 CM009241.2_SAMEA4374779: T:  302 C:  167 A: 3218 G:    0 -:   44    
Sequence : 21 CM009241.2_SAMEA4374780: T:  292 C:  169 A: 3209 G:    0 -:   61    
Sequence : 22 CM009241.2_SAMEA4374781: T:  308 C:  164 A: 3238 G:    0 -:   21    
Sequence : 23 CM009241.2_SAMEA4374782: T:  310 C:  170 A: 3239 G:    0 -:   12    
Sequence : 24 CM009241.2_SAMEA4374785: T:  306 C:  170 A: 3239 G:    0 -:   16    
Sequence : 25 CM009241.2_SAMEA4374788: T:  296 C:  168 A: 3203 G:    0 -:   64    
Sequence : 26 CM009241.2_SAMEA4374789: T:  282 C:  167 A: 3182 G:    0 -:  100    
Sequence : 27 CM009241.2_SAMEA4374790: T:  243 C:  161 A: 3149 G:    0 -:  178    
Sequence : 28 CM009241.2_SAMEA4374791: T:  281 C:  170 A: 3216 G:    0 -:   64    
Sequence : 29 CM009241.2_SAMEA4374792: T:  242 C:  165 A: 3156 G:    0 -:  168    
Sequence : 30 CM009241.2_SAMEA4374793: T:  233 C:  163 A: 3143 G:    0 -:  192    
Sequence : 31 CM009241.2_SAMEA4374794: T:  281 C:  165 A: 3177 G:    0 -:  108    
Sequence : 32 CM009241.2_SAMEA4374795: T:  223 C:  167 A: 3146 G:    0 -:  195    
Sequence : 33 CM009241.2_SAMEA4374796: T:  265 C:  162 A: 3178 G:    0 -:  126    
Sequence : 34 CM009241.2_SAMEA4374797: T:  275 C:  170 A: 3198 G:    0 -:   88    
Sequence : 35 CM009241.2_SAMEA4374798: T:  274 C:  173 A: 3208 G:    0 -:   76    
Sequence : 36 CM009241.2_SAMEA4374799: T:  277 C:  170 A: 3207 G:    0 -:   77    
Sequence : 37 CM009241.2_SAMN01920517: T:  233 C:  159 A: 3139 G:    0 -:  200    
Sequence : 38 CM009241.2_SAMN01920518: T:  217 C:  151 A: 3090 G:    0 -:  273    
Sequence : 39 CM009241.2_SAMN01920519: T:  213 C:  153 A: 3117 G:    0 -:  248    
Sequence : 40 CM009241.2_SAMN01920520: T:  236 C:  158 A: 3131 G:    0 -:  206    
Sequence : 41 CM009241.2_SAMN01920521: T:  227 C:  158 A: 3149 G:    0 -:  197    
Sequence : 42 CM009241.2_SAMN01920522: T:  215 C:  154 A: 3103 G:    0 -:  259    
Sequence : 43 CM009241.2_SAMN01920523: T:  224 C:  170 A: 3139 G:    0 -:  198    
Sequence : 44 CM009241.2_SAMN01920524: T:  232 C:  157 A: 3124 G:    0 -:  218    
Sequence : 45 CM009241.2_SAMN01920525: T:  237 C:  169 A: 3148 G:    0 -:  177    
Sequence : 46 CM009241.2_SAMN01920526: T:  230 C:  161 A: 3128 G:    0 -:  212    
Sequence : 47 CM009241.2_SAMN01920527: T:  236 C:  160 A: 3104 G:    0 -:  231    
Sequence : 48 CM009241.2_SAMN01920528: T:  224 C:  151 A: 3100 G:    0 -:  256    
Sequence : 49 CM009241.2_SAMN01920529: T:  194 C:  136 A: 3009 G:    0 -:  392    
Sequence : 50 CM009241.2_SAMN01920530: T:  204 C:  137 A: 2723 G:    0 -:  667    
Sequence : 51 CM009241.2_SAMN01920531: T:  222 C:  155 A: 2923 G:    0 -:  431    
Sequence : 52 CM009241.2_SAMN01920532: T:  206 C:  147 A: 2777 G:    0 -:  601    
Sequence : 53 CM009241.2_SAMN01920533: T:  207 C:  128 A: 2843 G:    0 -:  553    
Sequence : 54 CM009241.2_SAMN01920534: T:  206 C:  143 A: 2766 G:    0 -:  616    
Sequence : 55 CM009241.2_SAMN01920535: T:  211 C:  148 A: 2810 G:    0 -:  562    
Sequence : 56 CM009241.2_SAMN01920536: T:  213 C:  140 A: 2883 G:    0 -:  495    
Sequence : 57 CM009241.2_SAMN01920537: T:  246 C:  160 A: 3083 G:    0 -:  242    
Sequence : 58 CM009241.2_SAMN01920538: T:  228 C:  145 A: 2869 G:    0 -:  489    
Sequence : 59 CM009241.2_SAMN01920539: T:  242 C:  169 A: 3074 G:    0 -:  246    
Sequence : 60 CM009241.2_SAMN01920540: T:  241 C:  168 A: 3082 G:    0 -:  240    
Sequences read succesfully         
15000.000000
Run-time error      
Likelihood file for different no. seqs than data      
..now exiting to system...

Thanks

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