# Definition of callRate per sample

**URL:** <https://discuss.hail.is/t/definition-of-callrate-per-sample/572>\
**Category:** Hail Query & hailctl\
**Created:** [July 16, 2018, 8:31pm UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572 "2018-07-16T20:31:38Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![trptyrphe](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/trptyrphe/32/263_2.png) [@trptyrphe](https://discuss.hail.is/u/trptyrphe)\
**Post date:** [July 16, 2018, 8:31pm UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572/1 "2018-07-16T20:31:38Z")

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Hi,

How do you define call rate per sample vs call rate per variant? Say I have a vds of 100 samples by 10,000 variants.

If sample 1 has genotypes being called on 9,000 out of the 10k variants, does sample.callrate = 0.9?

If variant 1 has being detected in 50 out of the 100 samples, does variant.callrate = 0.5?

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**Author:** ![jbloom](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/jbloom/32/109_2.png) [@jbloom](https://discuss.hail.is/u/jbloom)\
**Post date:** [July 16, 2018, 8:44pm UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572/2 "2018-07-16T20:44:57Z")

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Yes, in both cases callRate is the proportion of calls that are non-missing. For variants, it’s measured per row. For samples, it’s measured per column.

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**Author:** ![trptyrphe](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/trptyrphe/32/263_2.png) [@trptyrphe](https://discuss.hail.is/u/trptyrphe)\
**Post date:** [July 16, 2018, 9:58pm UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572/3 "2018-07-16T21:58:07Z")

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Thanks, and I found the minor allele frequency from the variant.qc.AF metrics doesn’t center around 0 (homozygous) and 0.5 (heterozygous) as I expected, any explanation?

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**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 16, 2018, 10:12pm UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572/4 "2018-07-16T22:12:24Z")

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homozygosity and heterozygosity are properties of genotype calls, but AF is a property of all the genotypes at one variant.

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**Author:** ![trptyrphe](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/trptyrphe/32/263_2.png) [@trptyrphe](https://discuss.hail.is/u/trptyrphe)\
**Post date:** [July 17, 2018, 11:52am UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572/5 "2018-07-17T11:52:25Z")

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I understand that. So for a variant being called at multiple samples (a mix of het or hom ref or hom alt), how’s this field defined? Thanks.

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**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 17, 2018, 12:12pm UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572/6 "2018-07-17T12:12:35Z")

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The alleles of the genotype call don’t matter. If the genotype is called at all (not ./. in VCF) then it counts as called.

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<div class="post-metadata">

**Author:** ![trptyrphe](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/trptyrphe/32/263_2.png) [@trptyrphe](https://discuss.hail.is/u/trptyrphe)\
**Post date:** [July 17, 2018, 1:53pm UTC](https://discuss.hail.is/t/definition-of-callrate-per-sample/572/7 "2018-07-17T13:53:15Z")

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Sorry I wasn’t clear about my question: how’s the va.qc.AF field defined. Say we have a total of 3 samples. 1 sample is 0/0, 1 sample is 0/1, and 1 sample is 1/1. is the AF = 0.5 (3 alt alleles /6 possible alleles) or 2/3 (2 out of the 3 samples genotypes being called? Thanks.