[BioC] a workflow of population genomic operations/analysis using bioconductor

[Mao Jianfeng]

Dear bioconductor listers,

I just move from classical population genetics to genomics/population
genomics. I need to set up my genomic handling platform and ability. I
have used R for statistics for 3 years, so bioconductor is preferable
to me.

In my current study, we sequenced genomes of tens of accessions of a
plant, by Illumina next generation sequencer. And, now the reads have
been aligned with the reference genome.

I have not any experiences of genomic analysis. On the beginning, I
checked all the available packages for sequence analyses of the
bioconductor, and read their manual. And also, I surveyed the courses
in bioconductor websites. But, I still can not make a full and
effective workflow for me to do population genomic analysis, though I
have witnessed much excellent genomic implements of bioconductor.

I think an effective workflow to do population genomic analysis by
using R platform is very valuable for all of us who are/will be
genomicers. Thank you for your helps in advance.

I need hints, tips, suggestions, and advice on making an explicit and
effective workflow for me to do the following analysis by using
bioconductor or maybe not:

1. mutation types. e.g. CG -> AT, CG -> TA etc. polarized with the
relative genomes
2. Polymorphism along chromosomes (or scaffold)
3. Polymorphism by type; intergenic, CDs etc.; and polymorphism by
metabolic network
4. LD and recombination
5. drastic mutations. e.g. stop codons etc. in gene family, Gene Ontology
6. Population structure using STRUCTURE
7. Fst among groups
8. association studies

-- 
Jian-Feng, Mao