Could anybody explain briefly the main steps in IndelRealigner? My understand is sort of as follow, but I am not sure if it is true.
Step1: for each interval, find all the associated reads which have overlap with the interval;
Step2: get the "leftmost" and "rightmost" points of those reads. all the known Indels in the [leftmost, rightmost] interval will be deemed as confirmed indels.
Step3: traverse those reads, find ones which have and only have one indel and left-align the indels. All these indels will be deemed as candidate indels.
Step4: filter all the candidate indels and find ones which should really be good enough to add to confirmed indel list. (How?)
Step5: realign around the indels found from Step2 (KnownIndels) and Step4 (Filtered out Indels). (How?)
Did I understand the main steps correctly? How to do the Step 4 and 5?
Thanks very much.