Pairwise FST by population table and plot starting from vcf file
- R
- "SNPRelate" Rpackage (bioconductor)
- VCF input file
- Population metadata tab separated text input file ('samples' and 'pop' columns required). Here an example:
| samples | pop |
|---|---|
| Sample_1 | BIS |
| Sample_2 | BIS |
| Sample_3 | CEL |
| Sample_4 | CEL |
| Sample_5 | CHM |
| Sample_6 | CHM |
- Pairwise FST matrix example:
| BIS | CEL | CHM | |
|---|---|---|---|
| BIS | 0 | 0.15 | 0.22 |
| CEL | 0.15 | 0 | 0.26 |
| CHM | 0.22 | 0.26 | 0 |
This is an example of paiwise FST table with invented values just to match the example metadata table above and the Arlequin's plot below
- Arlequin's plot example:
This plot is an example of a pairwise FSTplot from Gama et. al. 2013 paper. The Arlequin's pairFstMatrix.r function used here produces this kind of output.
- FST calculation is performed using "SNPRelate" bioconductor Rpackage
- Pairwise FST matrix PLOT : is performed using Arlequin's pairFstMatrix.r (Author: Heidi Lischer) with very few edits
- Negative Fst are technical artifact of the computation (see Roesti el al. 2012) and are automatically replaced with zero.
Author: Riccardo Giannico - Date: 2017