Ask me for the most current version of these if you want to use them.
Several people in the lab are now working with very similar data (in structure) and have similar questions (in technique). As I have discussed with several people it would be very useful if we could all build up and share the tools needed to do these analysis. Understandably, people may want to do things on their own or in a specific manner, but I think there are several advantages to building this up together. The main thing is that it will be more efficient in terms of personnel time, having each person re-invent the wheel does not make sense. I think the blog is a great place to set do this. Below we can make our wish list and link to posts for solutions as they become available. As always, the principles (1,2 and 3) covered here apply.
1. Calling SNPs from alignments –ML approach perl– -samtools- -Genome tool kit-
2. Make a SNP table –shell script–
3. Clean the SNP table –SNP table parsing Perl–
4. Site by site statistics -R(fst etc, possibly best in all one script?)- -fst with perl-
5. Sliding window approaches -(Greg_B has a start of one will post)-
6. Other -Introgress (GB, will post)- -Structure-
Greg_B and …