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