| Class | Description |
|---|---|
| AnnotateIntervals |
Annotates intervals with GC content, and optionally, mappability and segmental-duplication content.
|
| CallCopyRatioSegments |
Calls copy-ratio segments as amplified, deleted, or copy-number neutral.
|
| CollectAllelicCounts |
Collects reference and alternate allele counts at specified sites.
|
| CollectAllelicCountsSpark |
See
CollectAllelicCounts. |
| CollectReadCounts |
Collects read counts at specified intervals.
|
| CreateReadCountPanelOfNormals |
Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel.
|
| DenoiseReadCounts |
Denoises read counts to produce denoised copy ratios.
|
| DetermineGermlineContigPloidy |
Determines the integer ploidy state of all contigs for germline samples given counts data.
|
| FilterIntervals |
Given specified intervals, annotated intervals output by
AnnotateIntervals, and/or counts output by
CollectReadCounts, outputs a filtered Picard interval list. |
| GermlineCNVCaller |
Calls copy-number variants in germline samples given their counts and the corresponding output of
DetermineGermlineContigPloidy. |
| ModelSegments |
Models segmented copy ratios from denoised read counts and segmented minor-allele fractions from allelic counts.
|
| PostprocessGermlineCNVCalls |
Postprocesses the output of
GermlineCNVCaller and generates VCF files as well as a concatenated denoised
copy ratio file. |
| PreprocessIntervals |
Prepares bins for coverage collection.
|
| Enum | Description |
|---|---|
| CollectReadCounts.Format | |
| DetermineGermlineContigPloidy.RunMode | |
| GermlineCNVCaller.RunMode |