Convenience scripts for preparing VCF files for input into the R package 'rehh'. These functions perform all the necessary pre-processing to go from a VCF file to extended haplotype homozygosity statistics (EHH, iHS).
- R and the package 'rehh'
- The phasing software 'Shapeit'
- A VCF file of genotypes
- A genetic map file with the following format:
| chrom | pos1 | pos2 | gen1 | gen2 | rate |
|---|---|---|---|---|---|
| 1 | 715797 | 956634 | 0.0000002 | 0.711856 | 2.955757629 |
Where:
- chrom = name of a chromosome (only numerics accepted, so far)
- pos1 = first physical position (bp)
- pos2 = second physical position (bp)
- gen1 = first map position (cM)
- gen2 = second map position (cM)
- rate = recombination rate (cM/MB)
Implictly, this also requires your VCF to be reference-based and your genetic map to correspond to the genomic coordinates in your VCF.