tsconvert

Utilities for converting tskit tree sequences to and from other formats.

tsconvert is in early development

Roadmap for v0.1

• Where conversion methods are widely used and do not require any dependencies, they will be implemented in tskit, for example writing VCF. tsconvert can then call the tskit method so that it has a complete list. Methods that require dependancies will be implemented here to avoid dependency bloat in tskit.

• Provide either to_, from_ (or both as appropriate) methods for the following formats:

• vcf

• ms

• argon

• newick

• newick + csv/tsv metadata

• nexus

• sgkit

• Where a format doesn't provide a full tree sequence it will have a parse_ method:

• plink (pedigree)

• Allow these methods to be used from the CLI, including streams.