# \[Breaking change\] Variant QC changes to support multiallelics

**URL:** <https://discuss.hail.is/t/breaking-change-variant-qc-changes-to-support-multiallelics/512>\
**Category:** Updates\
**Created:** [May 29, 2018, 9:51pm UTC](https://discuss.hail.is/t/breaking-change-variant-qc-changes-to-support-multiallelics/512 "2018-05-29T21:51:56Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [May 29, 2018, 9:51pm UTC](https://discuss.hail.is/t/breaking-change-variant-qc-changes-to-support-multiallelics/512/1 "2018-05-29T21:51:57Z")

</div>

We’ve changed [`hl.variant_qc`](https://hail.is/docs/devel/methods/genetics.html?highlight=variant_qc#hail.methods.variant_qc) to support multiallelics. This involves breaking changes to the schema produced. For instance, AF and AC are now arrays that include the reference allele. The GQ and DP statistics are also now not generated at all if those fields don’t exist.

Click through to the docs above to see the full story!

[build will take a few minutes to update]

---

<div class="post-metadata">

**Author:** ![jjfarrell](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/jjfarrell/32/108_2.png) [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\
**Post date:** [July 6, 2018, 8:38pm UTC](https://discuss.hail.is/t/breaking-change-variant-qc-changes-to-support-multiallelics/512/2 "2018-07-06T20:38:53Z")

</div>

It would also be useful to include MAF (minor allele frequency) metric when generating the variant\_qc stats. The Hail tutorials seem to assume the AF is actually the MAF when screening out low frequency variants. But there are rare variants that are the REF allele and these get left in after filtering for AF \< 0.01 instead of MAF \< 0.01.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 6, 2018, 8:53pm UTC](https://discuss.hail.is/t/breaking-change-variant-qc-changes-to-support-multiallelics/512/3 "2018-07-06T20:53:14Z")

</div>

MAF is `hl.min(mt.variant_qc.AF)`

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 6, 2018, 8:53pm UTC](https://discuss.hail.is/t/breaking-change-variant-qc-changes-to-support-multiallelics/512/4 "2018-07-06T20:53:32Z")

</div>

well, that’s the rarest allele at least.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 6, 2018, 8:53pm UTC](https://discuss.hail.is/t/breaking-change-variant-qc-changes-to-support-multiallelics/512/5 "2018-07-06T20:53:54Z")

</div>

good idea to change the tutorial though