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 (she/her)

    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 The usage example is out of date and we will get that documentation changed in the next GATK release.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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