Individual versus joint variant calling

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Priyadarshini Thirunavukkarasu

• November 03, 2021 08:31
• Edited

Hello

I need a suggestion. I have exome data of 6 subjects. As the sample size is very less, should we do variant calling on every sample rather than joint variant calling?. As joint variant calling on few subjects would lead to false positives

Thanks

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  Pamela Bretscher

  • November 03, 2021 13:00

  Hi Priyadarshini Thirunavukkarasu,

  I would say that using joint calling, even with a low number of samples, would lead to more accurate results and fewer false positives than if you run each sample separately. You can read more about the benefits of joint calling here. I'm going to move your post to the general discussion topic as the germline topic is for reporting bugs and issues with GATK.

  Kind regards,

  Pamela

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