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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GATK4.1.5 mutect2 output issue

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    Bhanu Gandham

    Hi Xin Zheng

     

    Can you please share the IGV image of the bamout for the same region. 

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    Xin Zheng

    Hi Bhanu Gandham

    Thanks for your help.Here is the bamout result, and I wonder why DP and other information is zero.

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    David Benjamin

    Xin Zheng It would be useful to know the results of a few brief experiments.  Could you try adding the following parameters to your Mutect2 command (separately in different runs of Mutect2, not at the same time) on a small region and report back what happens to the variant site in each case?

    1.  -independent-mates

    2. -linked-de-bruijn-graph

    3.  -error-correction-log-odds 3.0

    Also, could you scroll down to the part of the bamout with the artificial reads representing the assembled haplotypes and post a screenshot?  The haplotypes are the long reads all starting and ending at the bounds of the assembly region with the "HP" sample tag.

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    Xin Zheng

    Bhanu Gandham Thank you for your advice. 1. When I use independent-mates, this unormal site be gone and the other sites look normal.

    Unfortunately I couldn't find parameters(2, 3)  in gatk4.1.5. Do they have other names

     

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    David Benjamin

    Xin Zheng, option 3 was in merged in the master branch on github but was not in the GATK 4.1.5 release.  My mistake.  However, it should work in the 4.1.6 release that came out yesterday.  Option 2 should work in both 4.1.5 and 4.1.6.  I'm not sure what is happening with that one.

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