assign

The assign command assigns inferred tracts to source populations using match-rate files.

It compares the match rates for the same tract across two or more sources. A tract is assigned only when one source has the unique highest match rate. Tied tracts, tracts with no valid maximum, and tracts not shared by all input files are not assigned.

Example

Users can assign source populations to the inferred tracts using the following command:

sstar2 assign --match-rate examples/results/sstar2.example.nean.match.rate.bed \
                           examples/results/sstar2.example.den.match.rate.bed \
              --source-name nean den \
              --output-prefix examples/results/sstar2.example

This generates two BED files: one for inferred tracts from Neanderthals and the other for inferred tracts from Denisovans.

Outputs

One BED file is written for each source name:

<output-prefix>.<source-name>.inferred.tracts.bed

Each output file is tab-separated and has no header:

chrom  start  end  sample  match_rate

A source-specific output file is created even if no tracts are assigned to that source.

Settings

Argument	Description
--match-rate	Match-rate BED files generated by sstar2 match.
--source-name	Source names corresponding to --match-rate files.
--output-prefix	Prefix for source-specific BED output files.