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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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Add preset 'DeepVariant_unfiltered', analogous to 'gatk_unfiltered', etc. #229

Closed tedyun closed 4 years ago

tedyun commented 4 years ago

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

coveralls commented 4 years ago

Coverage Status

Coverage remained the same at 93.404% when pulling ff9f9245269ce4214287b9876c44b141ed2a5b80 on tedyun:tedyun-dv-unfiltered into ca0e9b774c8006faa5c3d7659f89653bbbc92d6b on dnanexus-rnd:master.

mlin commented 4 years ago

Thanks @tedyun and apologies for the slow uptake on this

tedyun commented 4 years ago

No worries and thank you Mike!