Site Frequency Spectrum

This method calculates a site frequency spectrum using ANGSD. Please see ANGSD's tutorial page.

Basic Usage

To run this method, use the following command

angsd-wrapper SFS Site_Frequency_Spectrum_Config

where Site_Frequency_Spectrum_Config is the full path to the configuration file for the site frequency spectrum.

All inputs should be specified in Site_Frequency_Spectrum_Config.

This method does make use of Common_Config, those that are used are listed below:

Variable	Function
`SAMPLE_LIST` `GROUP_SAMPLES` on `dev`	A list of samples to be used in calculations
`SAMPLE_INBREEDING` `GROUP_INBREEDING` on `dev`	A list of inbreeding coefficients, where each line here corresponds to a line in `SAMPLE_LIST` or `GROUP_SAMPLES` on `dev`
`ANC_SEQ`	Path to ancestral sequence
`PROJECT`	Name given to all outputs in ANGSD-wrapper
`SCRATCH`	Place to store files, the full path is `SCRATCH/PROJECT/SFS`
`REGIONS`	Limit the scope of ANGSD-wrapper to certain regions

This method has no method-specifc variables

The parameters for this method can be tweaked as necessary, they have been set for optimal generalized function:

Parameter	Function
`DO_SAF`	Creates a site frequency spectrum
`UNIQUE_ONLY`	Use uniquely mapped reads only
`MIN_BASEQUAL`	Minimum base quality score
`BAQ`	Adjust Q scores around indels
`MIN_IND`	Minimum number of individuals needed to use this site
`GT_LIKELIHOOD`	Estimates genotype likelihoods
`DO_GLF`	Format of genotype likelihoods file
`MIN_MAPQ`	Minimum base mapping quality
`N_CORES`	Number of cores to use, please do not set above the limits of your system
`DO_MAJORMINOR`	Estimate major/minor alleles
`DO_GENO`	Peform genotype calling
`DO_MAF`	Calculate per-site frequencies
`DO_POST`	Calculate the posterior probability using per-site frequencies
`OVERRIDE`	If `true`, will recalculate files that already exist

Naming Scheme	Contents
`PROJECT_DerivedSFS`*	Final site frequency spectrum
`PROJECT_SFSOut.arg`	Details of arguments
`PROJECT_SFSOut.geno.gz`	Genotype calls
`PROJECT_SFSOut.mafs.gz`	Minor allele frequencies
`PROJECT_SFSOut.saf.gz`	Intermediate site frequency spectrum
`PROJECT_SFSOUT.saf.idx`	Index of intermediate site frequency spectrum
`PROJECT_SFSOut.saf.pos.gz`	Position data of the saf file

PROJECT_DerivedSFS can be visualized with the Shiny graphing interface. A web browser with a graphical user interface is required.