Calculating Ds/Dn Ratio Through Contig Snp Annotation

Question

[jackuser1979]

I am newbie to NGS

I have mapped my illumina reads to non-model assembled reference contigs. By variant calling I have VCF format with SNPs predicted per contig. I dont have any information on chromosome location, intron exon boundary position. I want to calculate synonymous nonsynonymous ratio. I think I should go for contig SNP annotation starting with blast with other model species, then try to find intron exon boundaries using gene prediction programme like Genscan and then I can calculate synonymous nonsynonymous ratio using SNPeff. Any suggestion for good workflow?

Answer 1

[Zev.Kronenberg]

You need to annotate your genome to get gene models.

Maker2 can annotate you genome. http://www.yandell-lab.org/

Based on the questions you are asking I can infer that you have a novel organism and a population data. I have worked on a project very similar. The work flow should be:

1) assemble

2) annotate the genome (Maker, other annotation pipelines)

3) align the population data to the assembled genome

4) call variants

5) clean variants

6) phase variants

7) make inferences about population genetics (Fst, DN/DS, Theta, ....)

Popgen analyses need to be at the end of this workflow.

[Biomonika (Noolean)]

What does it mean to phase variants, please?