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Revision as of 13:32, 10 March 2010
, 13:32, 10 March 2010→(10) Run thunder (hidden Markov model)
To-Do: <br> ** Include genotypes only for individuals that have sequence data
To-Do: <br> ** Include genotypes only for individuals that have sequence data
== (10) Run thunder (hidden Markov model) ==
== (10) Run thunder (hidden Markov model) ==
/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/
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:
<br>
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>
|}
*GAP btw 47-65Mb
