Common Config

The Common_Config file holds variables that are used by multiple methods in ANGSD-wrapper:

Variable	Function
GROUP_SAMPLES	A list of samples to be used in calculations
GROUP_INBREEDING	A list of inbreeding coefficients, where each line here corresponds to a line in GROUP_SAMPLES
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/<name of method>
REGIONS	Limit the scope of ANGSD-wrapper to certain regions
UNIQUE_ONLY	Use uniquely mapped reads only
MIN_BASEQUAL	Minimum base quality score
BAQ	Calculate base alignment quality
MIN_IND	Minimum number of individuals needed to use each site
GT_LIKELIHOOD	Calculate 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	Determine major and minor alleles
DO_GENO	Call genotypes from genotype likelihoods. See this for further information.
DO_MAF
DO_POST	Calculates posterior probabilities