Total depth of coverage per sample and over all samples (DP)
Category Variant Annotations
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.
--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
--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 [ [ -∞ ∞ ] ]
--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 ∞ ] ]
GATK version 4.2.5.0-SNAPSHOT built at Mon, 7 Feb 2022 11:18:01 -0500.
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