Companion files¶

Populations file¶

Description

The populations file is used to assign individuals to populations. For pairwise statistics (dxy and fst), all pairwise comparisons between populations are generated. It is specified at the command line with the --populations argument.

Format

A headerless, tab separated file with the first column containing the sample name (as represented in the VCF), and the second column containing an arbitary population ID.

Example

ERS223827   BFS
ERS223759   BFS
ERS223750   BFS
ERS223967   AFS
ERS223970   AFS
ERS223924   AFS
ERS224300   AFS
ERS224168   KES
ERS224314   KES

BED file¶

Description

The BED file is used to manually defined genome regions over which to calculate summary statistics. It is specified at the command line with the --bed_file.

Note that pixy expects intervals to be one indexed, not zero indexed as many typical BED files are. If your BED file is zero indexed, you’ll need to convert the intervals (e.g. by adding 1 to the start and end).

Format

A headerless, tab separated file with the first column containing a chromosome ID, the second column containing the first position of a window, and the third column containing the last potion of the window. Each row = one window.

Example

X   1       10000
X   10001   20000
X   20001   30000
X   30001   40000
X   40001   50000
X   50001   60000
1   1       10000
1   10001   20000
1   20001   30000
1   30001   40000
1   40001   50000
1   50001   60000

Sites file¶

Description

The sites is used to restrict calculations to specific sites (e.g. 4-fold degenerate sites, introns, etc.). It is specified at the command line with the --sites_file.

Format

A headerless, tab separated file with the first column containing a chromosome ID (CHROM), the second column containing the position (POS) of a single site. Each row = one site.

Example