Arguments

Below is the full list of arguments accepted by pixy. You can also see the canonical help text at any time with pixy --help.

Required

--stats [pi|dxy|fst|watterson_theta|tajima_d]

Which statistics to calculate from the VCF. Provide one or more, separated by spaces. For example, --stats pi fst will compute π and F_ST.

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

Path to the input VCF. The VCF must be bgzipped and indexed with tabix (.tbi) or with bcftools index (.csi).

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

Path to a headerless, tab-separated populations file with columns [SampleID Population]. See Companion files for the exact format.

In addition, one of

--window_size [integer]

Window size, in base pairs, over which to calculate statistics. Window coordinates are determined automatically across the chromosomes selected.

--bed_file [path/to/regions.bed]

Path to a headerless BED file containing custom regions (chrom, chromStart, chromEnd) over which to compute the statistics. Useful when windows must match a specific genomic feature set (genes, introns, etc.) and may be heterogeneous in size.

Optional

--n_cores [integer]

Number of CPUs to use for parallel processing (default: 1).

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

Folder where output will be written. Defaults to the current working directory.

--output_prefix [prefix]

Prefix for output file(s). For example --output_prefix run1 produces [output_folder]/run1_pi.txt and so on. Defaults to pixy.

--chromosomes ['list,of,chromosomes']

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

--interval_start [integer]

Start position of an interval to restrict the analysis to. Only valid when computing over a single chromosome. Defaults to position 1.

--interval_end [integer]

End position of an interval to restrict the analysis to. Only valid when computing over a single chromosome. Defaults to the last position on the chromosome.

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

Path to a headerless, tab-separated file with columns [CHROM POS] defining the sites over which statistics should be calculated. Can be combined with --window_size and --bed_file.

--chunk_size [integer]

Approximate number of sites to read from the VCF at a time (default: 100000). Smaller values reduce memory use; larger values reduce I/O overhead.

--fst_type [wc|hudson]

F_ST estimator to use: wc (Weir & Cockerham 1984) or hudson (Hudson 1992 / Bhatia et al. 2013). Defaults to wc.

--include_multiallelic_snps

Include sites with more than two alleles in the calculation. Disabled by default because biallelic-only mode is slightly faster. Added in pixy 2.0.

--bypass_invariant_check

Skip the check that ensures invariant sites are present in the VCF. Disabled by default. Use with extreme caution. Without invariant sites, estimates of π and d_xy are systematically biased and will be wrong unless your data are simulated.

--silent

Suppress all console output.

--version

Print the pixy version number and exit.

--citation

Print the pixy citation and exit.

--help

Print the full help message and exit.

Example

A typical multi-statistic run including the new Watterson's θ and Tajima's D estimators:

pixy --stats pi fst dxy watterson_theta tajima_d \
--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