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Rescale genetic polymorphism data to match a common sample size.
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README.md

SoFoS

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

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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 -f -a 1.0 -b 1.0 -n 9

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.
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