Changes

From Genome Analysis Wiki
Jump to: navigation, search

1000 Genomes Project Pilot 1 SNP Calling

864 bytes added, 12:32, 10 March 2010
(10) Run thunder (hidden Markov model)
To-Do: <br> ** Include genotypes only for individuals that have sequence data
== (10) Run thunder (hidden Markov model) ==
/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:
chr<br>
{| cellspacing="1" cellpadding="1" border="1" style="width: 634px; height: 251px;"|-| 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>|}
5&nbsp;*GAP btw 47-67-865Mb
9*
 
10-12
13-15
212
edits

Navigation menu