admixture.py: Admixture Analysis

Automates the estimation of individual ancestries using Admixture. The functions allows for input as: i) Binary-PED files or ii) PED 12-formatted files. The function is also capable of configuring the optional arguments of Admixture.

Command-line Usage

The admixture automater may be called using the following command:

admixture.py

Example usage

Estimating individual ancestries for each sample within hapmap3.bed for three ancestral populations.

admixture.py --binary-ped-prefix hapmap3 --pop 3

Dependencies

• Admixture

Input Command-line Arguments

--ped-12-prefix <input_prefix>

Argument used to define the filename prefix shared by the 12-formatted ped file (.ped) and the map file (.map). Should not be used alongside the specific file arguments (e.g. --ped).

--ped-12 <ped_filename>

Argument used to define the filename of the plink 12-formatted ped file (.ped). Must be called alongside --map. Cannot be called alongside --ped-prefix.

--map <map_filename>

Argument used to define the filename of the plink map file (.map). Must be called alongside --ped. Cannot be called alongside --ped-prefix.

--binary-ped-prefix <input_prefix>

Argument used to define the filename prefix shared by the binary ped file (.bed), the fam file (.fam), and the bim file (.bim). Should not be used alongside the specific file arguments (e.g. --binary-ped).

--binary-ped <binary_ped_filename>

Argument used to define the filename of the plink binary ped file (.bed). Must be called alongside --fam and --bim. Cannot be called alongside --binary-ped-prefix.

--fam <fam_filename>

Argument used to define the filename of the plink fam file (.fam). Must be called alongside --binary-ped and --bim. Cannot be called alongside --binary-ped-prefix.

--bim <bim_filename>

Argument used to define the filename of the plink bim file (.bim). Must be called alongside --binary-ped and --fam. Cannot be called alongside --binary-ped-prefix.

Output Command-line Arguments

--overwrite

Argument used to define if previous output should be overwritten.

Required Command-line Arguments

--pop <K_int>

Argument used to defines the number of ancestral populations.

--admix-method <em, block>

Argument used to define the algorithm to use. Two algorithm are supported: Block relaxation algorithm (block) or EM algorithm (em). By default, the Block relaxation algorithm is used.

Optional Command-line Arguments

--acceleration <acceleration_int>

Argument used to defines the value of quasi-Newton acceleration method.

--major-converge-likelihood <likelihood_float>

Argument used to define the major terminaton criterion. Halt when the log-likelihood increases by less than the specified value between iterations.

--major-converge-iter <iter_int>

Argument used to define the major terminaton criterion. Defines the maximum number of iterations.

--minor-converge-likelihood <likelihood_float>

Argument used to define the minor terminaton criterion. Halt when the log-likelihood increases by less than the specified value between iterations.

--minor-converge-iter <iter_int>

Argument used to define the minor terminaton criterion. Defines the maximum number of iterations.

--bootstrap <bootstrap_int>

Argument used to define the number of bootstrap replicates.

--random-seed <seed_int>

Argument used to define the seed value for the random number generator.

--threads <thread_int>

Argument used to define the number of threads to be used for computation.