Thetas

This method estimates Thetas values and other neutrality statistics. Please see ANGSD for full details on this method.

Note:

This method requires output from the site frequency spectrum to run

Please calculate a site frequency spectrum before estimating Thetas

Basic Usage

To run this method, use the following command

angsd-wrapper Thetas Thetas_Config

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

All inputs should be specified in Thetas_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/Thetas`
`REGIONS`	Limit the scope of ANGSD-wrapper to certain regions

This variable is specific to this method:

Variable	Function
`PEST`	The site frequency spectrum file, this should be the `DerivedSFS` file

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_IND1`	Minimum number of individuals needed to use this site
`GT_LIKELIHOOD`	Estimates genotype likelihoods
`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_MAF`	Calculate per-site frequencies
`OVERRIDE`	If `true`, will recalculate files that already exist
`SLIDING_WINDOW`	Enable sliding window analysis
`WIN`	Window size for sliding window analysis
`STEP`	Step size for sliding window analysis

Naming Scheme	Contents
`PROJECT_Diversity.arg`	Details of arguments
`PROJECT_Diversity.mafs.gz`	Minor allele frequencies
`PROJECT_Diversity.thetas.gz`	Diversity statistics
`PROJECT_Diversity.thetas.gz.bin`	Binary index of diversity statistics
`PROJECT_Diversity.thetas.gz.idx`	Index of diversity statistics
`PROJECT_Diversity.thetas.gz.pestPG`	Final Thetas estimations

PROJECT.thetas.graph.me can be visualized with the Shiny graphing interface. A web browser with a graphical user interface is required.