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

MergeVcfs (Picard) Follow

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    Skyler Kuhn

    Is there a preference for using

    java -jar picard.jar MergeVcfs


    gatk MergeVcfs

    or are the two commands functional equivalent?

    If the two commands are equivalent, can you update the documentation's usage/help information to include `gatk MergeVcfs`? It seems like the usage in version 4.2.X usage may have changed to where including an `=` in the `--INPUT` and `--OUTPUT` option causes a non-zero exit code. I guess you may have changed how you were handling argument parsing.

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