Discrepant frequencies flag in VCF files?

General
1

Hi,
is there any “Discrepant frequencies” flag in the VCF files, mirroring the online variant page warning (see below)? Could not find one e.g. in the

chr1-155039847-G-A entry in gnomad.joint.v4.1.sites.chr1.vcf.bgz
Thanks!
Vasily.

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1 Like
2

Hi Vasily,

Thanks for your question!

We don’t currently include a specific “Discrepant frequencies” flag in the VCF files that mirrors the warning you see on the online variant page. However, you can identify these variants using the stat_union_p_value, which is present in the VCF. Variants with a p-value from the contingency table test or CMH (Cochran-Mantel-Haenszel) test less than 10^-4 are flagged for users’ attention on the browser, as described in more detail in this section of the gnomAD documentation: Combined Frequency Stats.

If you’d like to generate similar flags, you can filter variants based on the stat_union_p_value using the same cutoff we apply on the browser.

Hope this helps!