Thetas

ANSGD Thetas (diversity stats) calculation. See ANGSD for full details on this method.

Before running this script

Note: This is a piggybacked method

Make sure you have run SFS, the output of which will be used as input for this one i.e. you should run:

bash ./scripts/SFS.sh ./scripts/SFS_TAXON.conf
bash ./scripts/THETAS.sh ./scripts/THETAS_TAXON.conf

with the proper taxon name filled in. See the method page for details on running SFS.

Input files

Scripts

• Script filename: THETAS.sh
• example config file: THETAS_TAXON.conf

Necessary input files

• results/TAXON_DerivedSFS output from SFS
• results/TAXON_SFSOut.mafs.gz output from SFS
• results/TAXON_SFSOut.saf output from SFS
• results/TAXON_SFSOut.saf.pos.gz output from SFS
• data/TAXON_samples.txt bam list
• data/TAXON_F.txt inbreeding coefficients

Output files

• results/TAXON_Diversity.thetas.gz diversity stats

Mandatory THETAS_TAXON.conf Variables

• DO_SAF create SFS (default=2)
• UNIQUE_ONLY uniquely mapped reads (default=1)
• MIN_BASEQUAL minimum base quality (default=20)
• BAQ adjust qscores around indels (as SAMtools) (default=1)
• 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_MAF calculate per site frequencies (default=1)
• DO_THETAS calculate diversity stats (default=1)
• OVERRIDE this variable will redo analyses. Set to false if you want to skip (default=false)
• SLIDING_WINDOW this variable, when set to true will enable sliding window analysis (default=false)
• WIN window size for sliding window analysis (default=50000)
• STEP step size for sliding window analysis (default=10000)

Optional THETAS_TAXON.conf Variables:

• UNIX_USER this variable fills in absolute paths for the rest of the config file and script. It should match the name of the user's home directory.
• PROJECT_DIR absolute path to the location of the analysis folder
• ANGSD_DIR=${PROJECT_DIR}/angsd
• ANC_SEQ the path to the ancestral sequence file
• REF_SEQ the path to the reference sequence file
• TAXON the name of the data being analyzed. The script will look for files in the data directory with this name. These files include: ${TAXON}_samples.txt and ${TAXON}_F.txt. If these files are not present, the script will not work correctly. ${TAXON}_samples.txt contains a list of paths to BAM files. Check the data folder for an example. ${TAXON}_F.txt contains inbreeding coefficients for each of these samples. Check the data folder for an example.