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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

problem with R library



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    Hi Laurent MANCHON

    It seems that gatk installation and R cannot communicate with each other properly. Can you try with a gatk conda environment installation or the docker image. I just recently performed a similar study and my conda environment installed R and local gatk works perfectly. 

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    Laurent MANCHON

    yes, i known.
    But it works fine with past version of GATK, 
    so, my solution was to use version with R-3.6.2

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    Eric Blanc

    Same problem here, using conda installed GATK version

    I am under the impression that the "--args" argument in not recognized by "Rscript".

    This is consistent with the help page from the Rscript command (at least for R versions 4.1 & above). My understanding is that Rscript is an alias for "R --slave --no-restore --file=<script.R> --args". Indeed the man page of "getopt" states that:

    If R was invoked directly via the “R” command, this corresponds to all argu-
    ments passed to R after the “–args” flag.
    If R was invoked via the “Rscript” command, this corresponds to all arguments
    after the name of the R script file.

    If that analysis were correct, then removing "--args" in PlotDenoisedCopyRatios and PlotModeledSegments should do the trick.


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    Gökalp Çelik

    Hi Eric Blanc

    Thank you for the valuable suggestion. I will move this issue to developers to discuss and implement an update depending on the discussion and result. 

    For the above problem it also looks like an incompatible getopts and optparse library issue with gatk therefore the user solved the problem by using an older version of R and gatk. Sometimes infrastructures may have incompatible software installed by default. Currently the docker image for gatk includes all required library and tool versions to function properly. Any problems happening with local installs may not happen with the docker version so we recommend using gatk docker image instead. 


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