| Interface | Description |
|---|---|
| GenotypeFilter |
An interface for classes that perform Genotype filtration.
|
| VariantFilter |
Interface for classes that can generate filters for VariantContexts.
|
| Class | Description |
|---|---|
| AlleleBalanceFilter |
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
|
| DepthFilter |
Filters out a record if all variant samples have depth lower than the given value.
|
| FilterApplyingVariantIterator |
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying
iterator.
|
| FilterVcf |
Applies a set of hard filters to Variants and to Genotypes within a VCF.
|
| FisherStrandFilter |
Filters records based on the phred scaled p-value from the Fisher Strand test stored in
the FS attribute.
|
| GenotypeQualityFilter |
Genotype filter that filters out genotypes below a given quality threshold.
|
| QdFilter |
Filters out sites that have a QD annotation applied to them and where the QD value is lower than a
lower limit.
|