| Interface | Description |
|---|---|
| ReadTransformer |
Classes which perform transformations from GATKRead -> GATKRead should implement this interface by overriding
SerializableFunction |
| VariantTransformer |
Classes which perform transformations from
VariantContext -> VariantContext
should implement this interface by overriding < VariantContext ,VariantContext>#apply(VariantContext)
Created by jonn on 6/26/18. |
| Class | Description |
|---|---|
| AdapterTrimTransformer |
Trims (hard clips) adapter sequences from read ends.
|
| BaseQualityClipReadTransformer |
Clips reads on both ends using base quality scores
|
| BaseQualityReadTransformer | |
| BQSRReadTransformer | |
| DRAGENMappingQualityReadTransformer |
Read transformer intended to replicate DRAGEN behavior for handling mapping qualities.
|
| DUSTReadTransformer |
Masks read bases and base qualities using the symmetric DUST algorithm
|
| IUPACReadTransformer |
A read transformer to convert IUPAC bases (i.e.
|
| MappingQualityReadTransformer |
A read transformer to modify the mapping quality of reads with MQ=255 to reads with MQ=60
|
| MisencodedBaseQualityReadTransformer |
Checks for and errors out (or fixes if requested) when it detects reads with base qualities that are not encoded with
phred-scaled quality scores.
|
| NDNCigarReadTransformer |
A read transformer that refactors NDN cigar elements to one N element.
|
| PalindromeArtifactClipReadTransformer |
Trims (hard clips) soft-clipped bases due to the following artifact:
When a sequence and its reverse complement occur near opposite ends of a fragment DNA damage (especially in the case
of FFPE samples and ancient DNA) can disrupt base-pairing causing a single-strand loop of the sequence and its reverse
complement, after which end repair copies the true 5' end of the fragment onto the 3' end of the fragment.
|
| SimpleRepeatMaskTransformer |
Masks read bases with a supra-threshold number of A/T's or G/C's within a given window size.
|
| StripMateNumberTransformer |
Removes /1 or /2 and any whitespace from the end of the read name if present
|