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variant prioritization and quality
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@brentp brentp released this 23 Apr 16:19
· 111 commits to master since this release
v0.1.7
bbbf10e

The smoove annotate command now adds a SHQ (Smoove Het Quality) tag to every sample format) a value of 4 is a high quality call and the value of 1 is low quality. -1 is non-het.
It also adds a MSHQ for Mean SHQ to the INFO field which is the mean SHQ score across all heterozygous samples for that variant.

As a first pass, users can look for variants with MSHQ > 3.

This value is created from a data-driven model of het quality trained on 603 samples in large pedigrees and on > 500 quartets.

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