# LA entry is "NA" when samples is hom-ref in VDS

**URL:** <https://discuss.hail.is/t/la-entry-is-na-when-samples-is-hom-ref-in-vds/4242>\
**Category:** Hail Query & hailctl\
**Created:** [February 25, 2026, 3:11pm UTC](https://discuss.hail.is/t/la-entry-is-na-when-samples-is-hom-ref-in-vds/4242 "2026-02-25T15:11:28Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![DBScan](https://avatars.discourse-cdn.com/v4/letter/d/bc79bd/32.png) [@DBScan](https://discuss.hail.is/u/DBScan)\
**Post date:** [February 25, 2026, 3:11pm UTC](https://discuss.hail.is/t/la-entry-is-na-when-samples-is-hom-ref-in-vds/4242/1 "2026-02-25T15:11:28Z")

</div>

Hi, I’m a bit struggling with formatting my VDS file from local to global. Currently I have to following code to transform my local entries `LAD` and `LGT` into their global equivalent:

```python
mt = vds.variant_data.annotate_entries(
  AD = hl.vds.local_to_global(vds.variant_data.LAD,
                              vds.variant_data.LA,
                              n_alleles=hl.len(vds.variant_data.alleles),
                              fill_value=0,
                              number="R")
)

# Transform local genotype to global
mt = mt.annotate_entries(GT = hl.vds.lgt_to_gt(mt.LGT, mt.LA))

# Densify to MT
mt = hl.vds.to_dense_mt(hl.vds.VariantDataset(vds.reference_data, mt))

```

The resulting `mt` has the following format:

```python
+----------------+------------+------+-----------------------+------+-------+
| locus | alleles | rsid | s | GT | GQ |
+----------------+------------+------+-----------------------+------+-------+
| locus<GRCh38> | array<str> | str | str | call | int32 |
+----------------+------------+------+-----------------------+------+-------+
| chr1:100000 | ["G","T"] | NA | "SAMPLE" | 0/0 | 81 |

```

```python
| AD | DP | LGT | LAD | LA |
+--------------+-------+------+--------------+--------------+
| array<int32> | int32 | call | array<int32> | array<int32> |
+--------------+-------+------+--------------+--------------+
| NA | 41 | 0/0 | [41] | NA |

```

The issue I’m having is that `LA` is a `NA` when the sample is hom-ref, and therefore `AD` is `NA` as well. What would be the easiest way to fix it?

I’ve tried the following snippet, with no luck:

```python
# Annotate AD: If it's missing, create a array of length two with LAD, and DP - LAD
mt=mt.annotate_entries(AD=hl.or_else(mt.AD,hl.array([mt.LAD[0],mt.DP-mt.LAD[0]])))

```

Thanks!