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

Weird parameter of Depth of coverage (GATK4.1.7.0 beta version)

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    Genevieve Brandt

    Hi Henry, thanks for bringing this to our attention. The usage example is out of date and we will get that documentation changed in the next GATK release. 

    The -ct argument is an old argument from GATK3 and is now --summary-coverage-threshold.

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