Arguments

Below is a list of required and optional arguments that pixy accepts.

Required:

--stats [pi|fst|dxy]

Which statistics to calculate from the VCF (pi, dxy, and/or fst, separated by spaces)

--vcf [path/to/vcf.vcf.gz]

Path to the input VCF (bgzipped and tabix indexed).

--populations [path/to/populations_file.txt]

Path to the populations file. See quick start for format.

In addition, one of either:

--window_size [integer]

Window size in base pairs over which to calculate pi/dxy.

--bed_file [path/to/populations_file.txt]

Path to a headerless .BED file containing regions (chrom, chromStart, chromEnd) over which to calculate summary statistics

Optional arguments:

--n_cores [integer]

Number of CPUs to utilize for parallel processing (default=1).

--output_folder [path/to/output/folder]

Folder where output will be written, e.g. path/to/output_folder, defaults to current working directory.

--output_prefix [prefix]

Optional prefix for output file(s), e.g. ‘output’ will result in writing to [output folder]/output_pi.txt, defaults to ‘pixy’.

--chromosomes [‘list,of,chromosomes’]

A single-quoted, comma separated list of chromosome(s) (e.g. ‘X,1,2’). Defaults to all chromosomes in the VCF.

--interval_start [integer]

The start of a specific interval over which to calculate pi/dxy. Only valid when calculating over a single chromosome. Defaults to 1.

--interval_end [integer]

The end of a specific interval over which to calculate pi/dxy. Only valid when calculating over a single chromosome. Defaults to the last position for a chromosome.

--sites_file [path/to/sites_file.txt]

Path to a tab separated file containing a headerless list of sites (CHROM, POS) to (exclusively) include in calculations

--chunk_size [integer]

Approximate number of sites to read from VCF at any given time. Defaults to 100000. Smaller numbers can reduce memory use.

--fst_type [wc|hudson]

FST estimator to use, one of either: ‘wc’ (Weir and Cockerham 1984) or ‘hudson’ (Hudson 1992, Bhatia et al. 2013). Defaults to ‘wc’

--bypass_invariant_check [no|yes]

Bypass the check for invariant sites. Use with caution!

--version

Print the pixy version number.

--citation

Print the citation for pixy.

--help

Print the help message.

--silent

Suppress all console output (flag, no value required).

An example:

pixy --stats pi fst dxy \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--window_size 10000 \
--n_cores 4 \
--output_folder output \
--output_prefix pixy_output