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Revision as of 13:21, 10 March 2010
, 13:21, 10 March 2010→(10) Run thunder (hidden Markov model)
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:
Total 150 jobs (50 jobs for each population)
chr
=====
1-2
3-4
5-6
7-8
9*
10-12
13-15
Total 150 jobs (50 jobs for each population)
== (11) Ligate thunder results for larger chromosomes ==
== (11) Ligate thunder results for larger chromosomes ==
