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Joint Genotyping Recommendation #198

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SophieS9 opened this issue Nov 28, 2023 · 0 comments
Open

Joint Genotyping Recommendation #198

SophieS9 opened this issue Nov 28, 2023 · 0 comments

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@SophieS9
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SophieS9 commented Nov 28, 2023 •
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I'm running DeepVariant Pepper on various samples from different trios. I need to carry out joint genotyping as I need to be aware of when a variant is homozygous reference and when there is poor confidence in a region so the variant couldn't be determined.

I've tried using GLNexus but there appears to be an issue with the format of the gVCF from pepper - see issue dnanexus-rnd/GLnexus#287

Are there any recommendations for different joint genotyping approaches?

Thanks!

Sophie
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