GATK realignment around local indel algorithm
Hi GATK team,
Though I have read the seminar slides for GATK indelrealignment, I still have no idear about how GATK does that for us, is there anyone can suggest? Say, give me a reference, or a brief ìntroduction.
Actually, what I care most is whether indelrealignment takes base quality into consideration.Thank you very much.