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The main steps in IndelRealigner

PengWeiPRCPengWeiPRC United StatesMember

Hello,

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.

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