org.bdgenomics.adam.algorithms
consensus
Abstract class for generating consensus sequences for INDEL realignment.
Singleton object for creating consensus generators.
Singleton object for creating consensus generators.
Consensus generators are used in INDEL realignment to generate the consensus sequences that reads are realigned against. We have three consensus modes:
* From reads: This mode looks at the read alignments for evidence of INDELs. Any INDEL that shows up in a read alignment is extracted and used to generate a consensus sequence. * From reads with Smith-Waterman: This mode discards the original read alignments and uses Smith-Waterman to locally realign the read. If this realignment leads to a read being aligned with an insertion or deletion against the reference, we generate a consensus sequence for the INDEL. * From knowns: In this mode, we use a set of provided INDEL variants as the INDELs to generate consensus sequences for.
Additionally, we support a union operator, that takes the union of several consensus modes.
Abstract class for generating consensus sequences for INDEL realignment.
INDEL realignment scores read alignments against the reference genome and a set of "consensus" sequences. These consensus sequences represent alternate alleles/haplotypes, and can be generated via a variety of methods (e.g., seen in previous projects --> 1kg INDELs, seen in read alignments, etc). This trait provides an interface that a consensus generation method should implement to provide it's consensus sequences to the realigner.