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Is it possible to use VariantRecalibrator with only one sample? (90,000 MuTect2 calls)

Hi, I want to filter variants (called with MuTect2) with VariantRecalibrator and ApplyVQSR GATK tools.

However, I have only one sample, with 90,000 variants called. Would this be enough for GATK VariantRecalibrator and ApplyVQSR tools to apply a good model and properly filter my variants?

I will be grateful for any suggestions :)

mutect2 vqsr gatk
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written by wiki97 • wiki97

Hi geneart$$, thank you very much for your answer!

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written by wiki97 • wiki97

1 answer

Hi wiki, VQSR is not recommended to be used when you have less number of samples and definitely not when you have 1 sample. Please see :https://gatk.broadinstitute.org/hc/en-us/articles/360037594511 However , you can pad the samples using samples from good database source like 1000G. GATK explains how to do that. One thing though you may want to dig more into their documentation as they have it all there but sort of needle in the haystack.

Hope this helps !

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written by geneart$$ • geneart$$

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