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Add preset 'DeepVariant_unfiltered', analogous to 'gatk_unfiltered', etc. #229

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merged 1 commit into from
Aug 13, 2020

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tedyun
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@tedyun tedyun commented Jul 20, 2020

Hi Mike,

I thought it'd be useful to have a DeepVariant preset that doesn't apply filters or genotype revision, called DeepVariant_unfiltered analogous to the existing presets gatk_unfiltered, xAtlas_unfiltered, etc. Some users wanted to experiment with the settings and to try out the "NOMOD" version themselves.

I copied the settings for DeepVariantWGS preset and just changed min_AQ1: 0, min_AQ2: 0, revise_genotypes: false.

Please let me know what you think. Thank you!

p.s. It's been a while since we last talked - hope you're staying safe and healthy :)

Thanks,
Ted

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Coverage Status

Coverage remained the same at 93.404% when pulling ff9f924 on tedyun:tedyun-dv-unfiltered into ca0e9b7 on dnanexus-rnd:master.

@mlin mlin merged commit be09d3d into dnanexus-rnd:master Aug 13, 2020
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mlin commented Aug 13, 2020

Thanks @tedyun and apologies for the slow uptake on this

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tedyun commented Aug 13, 2020

No worries and thank you Mike!

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3 participants