Genotype Likelihoods

ANSGD genotype likelihoods calculation. See ANGSD for full details on this method.

To use this method, you would run:

bash ./scripts/GL.sh ./scripts/GL_TAXON.conf

with the proper taxon name filled in.

• Script filename: scripts/GL.sh
• Configuration file file: scripts/GL_TAXON.conf

Input files

Scripts

• scripts/GL.sh
• scripts/GL_TAXON.conf

Necessary input files

• data/TAXON_samples.txt bam list
• data/TAXON_F.txt inbreeding coefficients

Output files

• results/TAXON_DerivedSFS

Mandatory SFS_TAXON.conf Variables

• TAXON

Optional SFS_TAXON.conf Variables

• DO_GENO call genotypes and set up output (default=7)
• UNIQUE_ONLY uniquely mapped reads (default=0)
• MIN_BASEQUAL minimum base quality (default=20)
• MIN_IND minimum number of individuals needed to use site (default=1)
• GT_LIKELIHOOD estimate genotype likelihoods (default=2)
• MIN_MAPQ minimum base mapping quality to use (default=30)
• N_CORES number of cores to use (default=32)
• DO_MAJORMINOR estimate major/minor alleles (default=1)
• DO_POST estimate posterior genotype probability (default=1)
• POST_CUTOFF posterior floor limit (default=0.95)
• DO_MAF calculate per site frequencies (default=2)
• SNP_PVAL p-value cutoff for calling SNPs (default=1e-6)