Genome Analysis Toolkit

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

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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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