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.

All inputs should be specified in Abbababa_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`	List of inbreeding coefficients, 1 value for each individual
`ANC_SEQ`	Ancestral sequence, possibly used as an outgroup (see below)
`REF_SEQ`	Reference sequence
`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
`UNIQUE_ONLY`	Use uniquely mapped reads only
`MIN_MAPQ`	Minimum base mapping quality
`MIN_BASEQUAL`	Minimum base quality score
`MIN_IND`	Minimum number of individuals needed to use this site
`N_CORES`	Number of cores to use, please do not set above the limits of your system

These variables are specific to this method:

Variable	Function
`OUTGROUP`	FASTA file to be used as the outgroup for Abbababa tests. If left empty,

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

Parameter	Function
`DO_COUNTS`	Flag to count allele frequencies
`DO_ABBABABA`	Run the Abbababa analysis
`REMOVE_TRANS`	Remove transitions
`BLOCKSIZE`	Number of sites in each chunk
`USE_LAST`	Use the last individual in the bam file as outgroup instead of a fasta file
`ENHANCE`	Use only sites where the reads for the outgroup has the same base for all reads. Only works with USE_LAST=1

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