malariagen_data.ag3.Ag3.view_alignments

Ag3.view_alignments(region: str | Region | Mapping, sample: str, visibility_window: int = 20000, init: bool = True)

Launch IGV and view sequence read alignments and SNP genotypes from the given sample.

Parameters

regionstr or Region or Mapping

Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript.

samplestr

Sample identifier.

visibility_windowint, optional, default: 20000

Zoom level in base pairs at which alignment and SNP data will become visible.

initbool, optional, default: True

If True, call igv_notebook.init().