Total depth of coverage per sample and over all samples (DP)

Category Variant Annotations

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Overview

AllelePseudoDepth specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Optional Tool Arguments
--dirichlet-keep-prior-in-count	false	By default we don't keep the prior use in the output counts ase it makes it easier to interpretthis quantity as the number of supporting reads specially in low depth sites. We this toggled the prior is included
--pseudo-count-weight-decay-rate	1.0	A what rate the weight of a read decreases base on its informativeness; e.g. 1.0 is linear decay (default), 2.0 is for quadratic decay
Advanced Arguments
--dirichlet-prior-pseudo-count	1.0	Pseudo-count used as prior for all alleles. The default is 1.0 resulting in a flat prior

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

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--dirichlet-keep-prior-in-count

By default we don't keep the prior use in the output counts ase it makes it easier to interpretthis quantity as the number of supporting reads specially in low depth sites. We this toggled the prior is included

boolean  false

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--dirichlet-prior-pseudo-count

Pseudo-count used as prior for all alleles. The default is 1.0 resulting in a flat prior

double  1.0  [ [ -∞  ∞ ] ]

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--pseudo-count-weight-decay-rate

A what rate the weight of a read decreases base on its informativeness; e.g. 1.0 is linear decay (default), 2.0 is for quadratic decay

double  1.0  [ [ 0  ∞ ] ]

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GATK version 4.2.6.0-SNAPSHOT built at Fri, 8 Apr 2022 12:41:23 -0700.