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update maf to af

Marek Szuba requested to merge github/fork/at7/update_vep_keys into master

Created by: at7

Description

We updated the return keys for the vep endpoints from *_maf to *_af. The change appears in the colocated variants section of the output hash.

Use case

Users want to know if their input variant has know frequency data. We report the frequency from co-located variants if the input allele matches one of the alleles of the colocated variant. We then add the frequency to the output. MAF stands for minor allele frequency. This is not always the case when we return the frequency. It is better to call it AF which just stands for allele frequency.

Benefits

Avoids confusion and sometimes naming errors. The allele frequency is not always the minor allele frequency. We made the change in the VEP script version and VEP tool. This would make our reporting more consistent across the VEP applications.

Possible Drawbacks

It is very likely that users have written parsers which filter for *_maf.

Testing

Have you added/modified unit tests to test the changes?

vep.t has been updated.

If so, do the tests pass/fail?

vep.t runs without errors.

  • tests fail on travis. not related to the PR's change.

Changelog

[/vep/:species/*] We updated the frequency keys in the collocated variants entry. The keys have been updated from *_maf to *_af. The new naming better reflects that we only report allele frequencies from co-located variants if the input allele is matched.

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