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Variant Discovery in High-Throughput Sequencing Data

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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

PoN: Mutect2 error

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    manolis

    I tested some WES and works. I also tested 4 WGS and for only one works, the other 3 have the same problem.

    For the WGS that does not work I have an output file (.vcg.gz, .tbi), of smaller sizes, and the tool does not create the stats file.

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    manolis

    I add a more general question:

    you advice to use in a pipeline the same tool version, for example when I go to use the Mutect2-TumorOnly pipeline I have to pre-process+PoN+Mutect2+downsteam somatic SNV tools with the same gatk version. I saw that you have a ready-to-use PoN file (from 1000g) and I used it with gatk v4130 and v4160 and I do not have any errors (I think that you created it with a very old gatk version). I created a PoN file with gatk v4130 and I used it with v4160, no errors.

    The point is, do you confirm me, in general, that for the final PoN files there is not any conflict between versions?

    Thanks

     

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    manolis

    Hi,

    I tested one of the 3 failed sample with the 4.1.3.0 version and I do not have any erro, related to my initial post.

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    Bhanu Gandham

    Hi manolis

    There are known bugs in the GATK v4.1.5.0 and v4.1.6.0 specifically affecting Mutect2 and HaplotypeCaller. take a look at this github issue ticket: https://github.com/broadinstitute/gatk/issues/6533

    This has been resolved in the v4.1.7.0. Can you please upgrade to the latest version and try again, That should resolve it.

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    manolis

    Thank you very much Bhanu Gandham, I will try the last version.

    Best

     

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    David Benjamin

    manolis We can confirm that using an older panel of normals with the latest GATK is fine.  

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    manolis

    Many thanks David Benjamin!

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