SoFoS

Rescale and smooth genetic polymorphism data to match a common sample size.

Usage

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

Notes

• 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