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Difference between variant calling and genotyping

Hi, I see these two terms interchangeably and then I see them next to each other. Can someone clarify the difference between the two? Thanks!

variant calling genotyping
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updated by Charles Warden Charles Warden • written by Floydian_slip Floydian_slip

my guess would be variant calling =~ probing for existence of alleles and genotyping ~= finding which alleles (allelic pair in diploids) exist in an individual.

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written by microfuge microfuge

another absolute gem from Kevin

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written by microfuge microfuge

2 answers

Thanks guys, this is very helpful.

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written by Floydian_slip Floydian_slip

I would tend to use genotyping for arrays (probably for germline variants), and variant calling for high-throughput sequencing (for either germline or somatic variants)

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written by Charles Warden Charles Warden

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