Lets say that you have whole genome variant calls for a number of individuals from a population within a species.
What are standard analysis / tools that you can always run out of the box after you get a a multi-sample vcf file?
- SNPEff -> Effect prediction, Ts/Tv ratio, Codon changes, Amino acid changes, Changes by chromosome
- SNPSifft - > filtering the SNPEff annotated data
- VCF-tools VCF-stats -> Number of private SNP per individual
- SNPRelate -> PCA plot, Phylogentic tree
I guess a lot of people are nowadays sequencing multiple individuals from a population and they all want to explore the variant calls / relation / contrast between individuals. Of course experiment, questions and populations are different but it is always good to minimize reinventing the wheel and maximizing usage of existing tools.
Things I am for example looking for are:
- plotting variant densities
- plotting LD plots