Rescale and smooth genetic polymorphism data to match a common sample size.
sofos [OPTION]... [FILE] > [OUTPUT]
With no FILE or when FILE is -, read standard input.
Input format is a VCF/BCF file with genotypes.
| Argument | Description |
|---|---|
| -a number -b number | shape parameters of beta prior |
| -n integer | number of gene copies in posterior resample |
| -f -u | generated (f)olded or (u)nfolded distributions |
| -t -r | use AA (t)ag or (r)eference allele as ancestral |
| -e number | probability of ancestral allele misassignment |
| -p [or] -pp | use GP tag to estimate allele frequencies |
| -z number | add extra invariant sites to manage ascertainment bias |
| -P number | average ploidy of samples (used with -z) |
| -q -v | (q)uiet progress info or be (v)erbose |
| -h | print usage information |
Defaults: sofos -u -a 1.0 -b 1.0 -n 10 -P 2
- Unless otherwise stated -f enables -r and -u enables -t.
- -p specifies that GP contains probabilities in the range 0 and 1.
- -pp specifies that GP contains phred-scaled probabilities.
- -e is only used for generating unfolded spectra.
- -n is the resampled population size