diff --git a/docs/how_do_i.rst b/docs/how_do_i.rst index 66912a17d..a00194591 100644 --- a/docs/how_do_i.rst +++ b/docs/how_do_i.rst @@ -62,6 +62,15 @@ Call :py:func:`display_genotypes`: sg.display_genotypes(ds, max_variants=10) +Get the reference allele? +---------------------- + +The specification for [VCFs stored in Zarr](https://github.com/pystatgen/vcf-zarr-spec/blob/main/vcf_zarr_spec.md) +places the REF allele as the first allele in the ``variant_allele`` array. For example, the following will print out all the REF alleles + +.. ipython:: python + + ds.variant_allele[:,0].values Subset the variables? ---------------------