Questions about IndelRealigner - Gap Open Penalty & Consensus
Dear GATK team,
I have two questions about IndelRealigner.
Can I adjust Gap open penalty for IndelRealigner?
As I understand, IndelRealigner make consensus alignments across the pre-existing alignments and aligns the reads to the consensus alignments.
When making the consensus alignment, is it right that IndelRealigner do multiple-alignment among the pre-existing alignments(or aligned reads)? Or does it picks some of the pre-existing alignments as consensus?
I could not find any document about how exactly the IndelRealigner does its job.
If there is any useful document, could you let me know?
Thank you very much!