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864 bytes added
, 13:32, 10 March 2010
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| To-Do: <br> ** Include genotypes only for individuals that have sequence data | | To-Do: <br> ** Include genotypes only for individuals that have sequence data |
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− | == (10) Run thunder (hidden Markov model) == | + | == (10) Run thunder (hidden Markov model) == |
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| /home/ylwtx/codes/cpp/mach-1.0.16/test_thunder/2009.09.all/ | | /home/ylwtx/codes/cpp/mach-1.0.16/test_thunder/2009.09.all/ |
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| Notes:<br>(1) Cleaned monomorphic sites before feeding to thunder (no need, b/c thunder 005 handles AL1/-)<br>(2) All sites are bi-allelic with one of the alleles being the reference allele (sites with more than 2 alleles including the reference allele are discarded at the beginning of thunder run: initially because of a prior dependent on the reference allele. In the current setting, where Freq1 is used for the prior, we can choose to ignore the reference allele information.) <br>a. Codes changed on 2009-11-02<br>(3) Split: | | Notes:<br>(1) Cleaned monomorphic sites before feeding to thunder (no need, b/c thunder 005 handles AL1/-)<br>(2) All sites are bi-allelic with one of the alleles being the reference allele (sites with more than 2 alleles including the reference allele are discarded at the beginning of thunder run: initially because of a prior dependent on the reference allele. In the current setting, where Freq1 is used for the prior, we can choose to ignore the reference allele information.) <br>a. Codes changed on 2009-11-02<br>(3) Split: |
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− | chr
| + | <br> |
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− | 1-2 | + | {| cellspacing="1" cellpadding="1" border="1" style="width: 634px; height: 251px;" |
− | 3-4 | + | |- |
| + | | chromosome |
| + | | #parts<br> |
| + | | length per part in Mb (last segment)<br> |
| + | | start<br> |
| + | | end<br> |
| + | |- |
| + | | 1-2<br> |
| + | | 4<br> |
| + | | 70 (63-67)<br> |
| + | | 0,60,120,180<br> |
| + | | 70,130,190,243-247<br> |
| + | |- |
| + | | 3-4<br> |
| + | | 4<br> |
| + | | 60 (41-49)<br> |
| + | | 0,50,100,150<br> |
| + | | 60,110,160,191-200<br> |
| + | |- |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | |- |
| + | | 5-6<br> |
| + | | 3<br> |
| + | | 70 (51-61)<br> |
| + | | 0,60,120<br> |
| + | | 70,130,171-181<br> |
| + | |- |
| + | | 7-8<br> |
| + | | 3<br> |
| + | | 60 (40-59)<br> |
| + | | 0,50,100<br> |
| + | | 60,110,140-159<br> |
| + | |- |
| + | | 9*<br> |
| + | | 3<br> |
| + | | 75, 45, 40<br> |
| + | | 0,'''65''',100<br> |
| + | | '''75''',110,140<br> |
| + | |- |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | |- |
| + | | 10-12<br> |
| + | | 2<br> |
| + | | 70 (72-75)<br> |
| + | | 0,60<br> |
| + | | 70,132-135<br> |
| + | |- |
| + | | 13-15<br> |
| + | | 2<br> |
| + | | 60 (50-64)<br> |
| + | | 0,50<br> |
| + | | 60,100-114<br> |
| + | |- |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | | <br> |
| + | |- |
| + | | 16-22<br> |
| + | | 1<br> |
| + | | 47-89<br> |
| + | | <br> |
| + | | <br> |
| + | |} |
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− | 5-6
| + | *GAP btw 47-65Mb |
− | 7-8
| |
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− | 9*
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− |
| |
− | 10-12
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− | 13-15
| |
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