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

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4 comments

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    Anup Agarwal

    What options need to be specified when spark is running over YARN in cluster mode. From what I understand, there is no spark daemon process listening for jobs, one simply submits jobs using spark-submit binary with the master as yarn and spark picks yarn config from $HADOOP_CONF_DIR. Is that mode not supported?

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    Anand

    Hi

    It looks like this below link listed on this page is broken:

    See the example parameters below and the local-Spark tutorial for more information

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    yh guo

    "Some GATK tools only exist in a Spark-capable version

    Those tools don't have the "Spark" suffix."

    Is it mean tools like CombineGVCFs can run with paremater of --conf 'spark.executor.cores=8'?

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    Jiten Parmar

    Is it possible to run spark workflows on multiple nodes? If yes, how?

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