What Is Difference Between Gatk And Dindel For Calling Indel

Question

[Zhaojing]

What is difference between GATK and Dindel for calling indel ,I see that in the GATK second step :discovery indel ,The genotype likelihoods calculation is inspired by Dindel.So I want to know the detail information about GATK and Dindel for calling indel .

Answer 1

[Zhaojing]

GATK call indel in the second step :use the unified genotype ,in this step , GATK use map/reduce model to increase the speed ,but the memory use too much .The test result :

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Dataset:A 10M ref extacted from chr22 of hg18 and 4X depth dataset of an individuals result: memory time Dindel 3M 349s GATK 1.2G 12s

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if you have the detail information ,I `m looking forward to hearing from you !