Thetas

Thetas

Note: you need to run SFS and get a .saf file before running thetas Script filename: ANGSD_Thetas.sh (includes Tajima's D) with defaults:

• 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)
• REGIONS chromosome and region to use (default="1:"). A regions file is also supported, just supply a path to the file for this variable. For example, REGIONS="${PROJECT_DIR}/data/regions.txt". The script will check for the presence of the / character in the REGIONS variable and use the appropriate flag in ANGSD.
• OVERRIDE this variable will redo analyses. Set to false if you want to skip
• SLIDING_WINDOW this variable, when set to true will enable sliding window analysis
• WIN window size for sliding window analysis
• STEP step size for sliding window analysis

no defaults (necessary in .conf):

• 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.