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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

(How to) Run GATK in a Docker container Follow

6 comments

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    vivekruhela

    Hi,

     

    Thanks for this tutorial. I have successfully pulled the gatk docker image as described above but when I tried this command 

    docker run -v ~/my_project:/gatk/my_data -it broadinstitute/gatk:4.1.3.0

    but I am getting an error of invalid mount specifications. '~/bam_files: gatk/my_data' invalid mount config for type "bind" : invalid mount path. mount path must be absolute. Kindly suggest.

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    Humphrey Gardner

    did you already create the "my_project" folder in your home directory?

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    vivekruhela

    Humphrey Gardner

    I tried it few months before. As far as I remember, I have already created the directory `bam_files` in my home directory and then I was trying to mount it to docker. I am not using docker now. I am using the java version of GATK in my work. Thanks.

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    François Kroll

    Incredibly helpful – thank you

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    Guy Horev

    That way one can work with GATK in interactive mode. To run gatk in a script I had to run docker in detached mode (adding -d flag). 

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    Ricardo Chinchilla

    How I can create the dict file inside Docker?. I try but I have this error: unable to access jarfile picard.jar

     

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