Genotype Likelihoods

Estimate genotype likelihood 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 Genotypes Genotype_Config

where Genotype_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 Genotype_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
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
REF_SEQ	Path to reference sequence
PROJECT	Name given to all outputs in ANGSD-wrapper
SCRATCH	Place to store files, the full path is SCRATCH/PROJECT/GenotypeLikelihoods
REGIONS	Limit the scope of ANGSD-wrapper to certain regions

Method-Specific Variables

This method has no method-specifc variables

Method Parameters

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

Parameter	Function
DO_MAJORMINOR	Estimate major/minor alleles
UNIQUE_ONLY	Use uniquely mapped reads only
MIN_MAPQ	Minimum base mapping quality
MIN_BASEQUAL	Minimum base quality score
GT_LIKELIHOOD	Estimate genotype likelihoods
DO_GENO	Call genotypes and setup the output
DO_POST	Estimate the posterior genotype probability
POST_CUTOFF	Floor limit for the posterior probability
DO_MAF	Calculate per-site frequencies
SNP_PVAL	P-value cutoff for calling SNPs
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

Output files

Naming Scheme	Contents
PROJECT_SFSOut.beagle.gz	Genotype likelihoods