From 188c9897a1ad9241c30b6fee7057c5c76245e831 Mon Sep 17 00:00:00 2001
From: Yan Wong <yan.wong@bdi.ox.ac.uk>
Date: Mon, 22 Jan 2024 13:49:17 +0000
Subject: [PATCH] Add getting REF to how_do_i

---
 docs/how_do_i.rst | 9 +++++++++
 1 file changed, 9 insertions(+)

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?
 ---------------------