# Split\_multi\_hts altering GQs

**URL:** <https://discuss.hail.is/t/split-multi-hts-altering-gqs/4102>\
**Category:** Hail Query & hailctl\
**Created:** [April 8, 2025, 12:58pm UTC](https://discuss.hail.is/t/split-multi-hts-altering-gqs/4102 "2025-04-08T12:58:51Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![Ruth\_Eberhardt](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/ruth_eberhardt/32/742_2.png) [@Ruth\_Eberhardt](https://discuss.hail.is/u/Ruth_Eberhardt)\
**Post date:** [April 8, 2025, 12:58pm UTC](https://discuss.hail.is/t/split-multi-hts-altering-gqs/4102/1 "2025-04-08T12:58:51Z")

</div>

Hi  
When running split\_multi\_hts on a matrixtable I am finding GQs are being changed, can someone explain this behaviour to me.  
I am happy to provide VCF and jupyter notebook for the below if you can advise me on how to share them with you (vcf is 372M).  
Details follow:

Running Hail version 0.2.134-952ae203dbbe  
I have a WGS VCF for 5 samples which has been variant called using DeepVariant and GLnexus.  
I first noticed a problem when producing histograms of GQ using the following command

```python
p = hl.plot.histogram(pcrfree_mt.GQ, range=(0,100), title='Ultima (PCRfree) GQ Histogram', legend='GQ')

```

The histrogram showed roughly the expected distribution

 ![Screenshot 2025-04-08 at 09.26.41](https://canada1.discourse-cdn.com/flex036/uploads/hail/original/2X/f/fd682b16ff1eadbabb7d98175078b0e5ff63175d.png)

I then split the multiallelics

```python
pcrfree_mt_split = hl.split_multi_hts(pcrfree_mt)

```

plotting the histogram after splitting showed \> 9 million variants with GQ ~98/99, which were not there in the dataset prior to splitting

 ![Screenshot 2025-04-08 at 13.48.16](https://canada1.discourse-cdn.com/flex036/uploads/hail/original/2X/1/1312c8b655131619d3b0657d461162e831276ca7.png)

The following is a screenshot from the output of mt.summarize.entries() from my unsplit data - this shows a maximum GQ of 90

 ![Screenshot 2025-04-08 at 09.29.22](https://canada1.discourse-cdn.com/flex036/uploads/hail/original/2X/5/524df8e80e28d8106a3c6f2c9daefd0e5f634e75.png)

This is a screenshot of mt.summarize.entries() from the data after split\_multi\_hts, showing the maximum GQ is now 99

 ![Screenshot 2025-04-08 at 09.30.09](https://canada1.discourse-cdn.com/flex036/uploads/hail/original/2X/6/6d4bdd343bfc3bc1a29cfa7dcc0452cf3894e692.png)

There are now 9723159 entries with GQ of \> 90. I checked a handful against the raw VCF and the GQ has definitely been altered.

The entries which now have a GQ of \>90 include entries which were split by split\_multi\_hts and entries which were not split.

```python
pcrfree_mt_split_highGQ = pcrfree_mt_split_highGQ.filter_rows(pcrfree_mt_split_highGQ.variant_qc.n_called > 1)
pcrfree_mt_split_highGQ.aggregate_rows(hl.agg.counter(pcrfree_mt_split_highGQ.was_split))

{False: 2849457, True: 294118}

```

I hope someone can help  
Best wishes  
Ruth