# Vep config hailctl dataproc

**URL:** <https://discuss.hail.is/t/vep-config-hailctl-dataproc/3005>\
**Category:** Hail Query & hailctl\
**Created:** [December 21, 2022, 9:13pm UTC](https://discuss.hail.is/t/vep-config-hailctl-dataproc/3005 "2022-12-21T21:13:17Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![arm](https://avatars.discourse-cdn.com/v4/letter/a/ce73a5/32.png) [@arm](https://discuss.hail.is/u/arm)\
**Post date:** [December 21, 2022, 9:13pm UTC](https://discuss.hail.is/t/vep-config-hailctl-dataproc/3005/1 "2022-12-21T21:13:17Z")

</div>

Hello,

I am attempting to create a customized config file for vep to run from a dataproc cluster created using hailctl.

The example config file given in the documentation at: [Hail | Genetics](https://hail.is/docs/0.2/methods/genetics.html#hail.methods.vep) works for me, but I would like to change the annotation to include a higher level field for gene\_symbol (right now it is nested under transcript\_consequences and returning NA values for most variants) and a field for all of the possible consequences of the variant. These are the --symbol and --summary flags in vep and mutually exclusive with the --everything flag used in this example.

How do I need to change the config file to make these changes?  
Thank you!

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<div class="post-metadata">

**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [December 21, 2022, 9:37pm UTC](https://discuss.hail.is/t/vep-config-hailctl-dataproc/3005/2 "2022-12-21T21:37:34Z")

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I think you’ll have an easier time extracting the gene\_symbol afterwards:

```python
ht = hl.vep(...)
ht = ht.annotate(
    gene_symbols = hl.set(ht.transcript_consequences.map(
        lambda tc: tc.gene_symbol
    ).filter(lambda x: hl.is_defined(x)))
)

```

Note that a given variant can reside in zero or more genes.

---

<div class="post-metadata">

**Author:** ![arm](https://avatars.discourse-cdn.com/v4/letter/a/ce73a5/32.png) [@arm](https://discuss.hail.is/u/arm)\
**Post date:** [December 21, 2022, 9:51pm UTC](https://discuss.hail.is/t/vep-config-hailctl-dataproc/3005/3 "2022-12-21T21:51:05Z")

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Thanks for the tip! I have tried this, but I also need to add fields to the vep annotation. Is there a way to request additional flags using the config file?  
Thanks!

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<div class="post-metadata">

**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [December 21, 2022, 9:59pm UTC](https://discuss.hail.is/t/vep-config-hailctl-dataproc/3005/4 "2022-12-21T21:59:50Z")

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The config file is for describing the output of VEP, unless you plan to change the VEP executable to produce a different kind of output, then you shouldn’t modify the config. EDIT: I see there are some flags. I’m not sure how to use those, but I recommend doing the following.

If you want the annotation to be under the vep annotation, do this:

```python
ht = hl.vep(...)
ht = ht.annotate(
    vep = ht.vep.annotate(
        gene_symbols = hl.set(ht.transcript_consequences.map(
            lambda tc: tc.gene_symbol
        ).filter(lambda x: hl.is_defined(x)))
    )
)

```

---

<div class="post-metadata">

**Author:** ![arm](https://avatars.discourse-cdn.com/v4/letter/a/ce73a5/32.png) [@arm](https://discuss.hail.is/u/arm)\
**Post date:** [December 21, 2022, 10:00pm UTC](https://discuss.hail.is/t/vep-config-hailctl-dataproc/3005/5 "2022-12-21T22:00:22Z")

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Ah, okay. Thank you!