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GATK realignment around local indel algorithm

liuxingliangliuxingliang SingaporeMember
edited January 2015 in Ask the GATK team

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.

bless~

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