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can't find the software Indelocator

I must use Indelocator to call short indels, the web cga says: It is a part of GATK distribution (although not officially supported by GATK team), and documentation and download instructions can be found at GATK Wiki.
If you are interested in the exact version of Indelocator used in "Sequence analysis of mutations and translocations across breast cancer subtypes" (submitted), please download this executable:
IndelGenotyper.36.3336-GenomeAnalysisTK.jar
This file is for breast cancer,but I use indelocator for gastric cancer.I really can't find other links for this software.
How can I get the software and manual ?

Best Answer

Answers

  • lyanliulyanliu OEMember

    @Geraldine_VdAuwera said:
    That information is out of date, indelocator is no longer distributed. Instead you should use MuTect2 which is part of GATK since version 3.5 and is able to call both SNVs and indels jointly.

    Thank u for your answer .I've tried the GATK 3.5,but it need few days to run although I have been used 20 threads .Are there any other ways to speed up?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Multithreading does not speed up MuTect substantially; you'd be better off implementing some scatter-gather parallelism using e.g. Queue.

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