Abbababa

This method calculates Abbababa statistics using ANGSD. Please see ANGSD's tutorial page for full details on this method.

Basic Usage

To run this method, use the following command

angsd-wrapper Abbababa Abbababa_Config

where Abbababa_Config is the full path to the configuration file for the 2D site frequency spectrum and Fst estimations.

Input files

All inputs should be specified in Abbababa_Config.

Common Variables

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
PROJECT	Name given to all outputs in ANGSD-wrapper
SCRATCH	Place to store files, the full path is SCRATCH/PROJECT/Abbababa
REGIONS	Limit the scope of ANGSD-wrapper to certain regions

Method-Specific Variables

These variables are specific to this method:

Variable	Function
OUTGROUP	FASTA file to be used as the outgroup for Abbababa tests

Method Parameters

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

Parameter	Function
DO_ABBABABA	Run the Abbababa analysis
REMOVE_TRANS	Remove transitions
UNIQUE_ONLY	Use uniquely mapped reads only
MIN_BASEQUAL	Minimum base quality score
MIN_IND	Minimum number of individuals needed to use this site
MIN_MAPQ	Minimum base mapping quality
N_CORES	Number of cores to use, please do not set above the limits of your system
BLOCKSIZE	Number of sites in each chunk

Output Files

Naming Scheme	Contents
PROJECT.abbababa.txt
PROJECT.D.abbababa
PROJECT.D.arg	Details of arguments

Visualization

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