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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Reported Mutect2 issue - Important information about GATK >= 4.1.8.1 Follow

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Laura Gauthier
  • Updated

🚨 Users have reported decreased Mutect2 variant calling accuracy in versions 4.1.8.1 and later🚨

We suspect the issue results from an update making Mutect2 more sensitive to particular edge cases, which are not represented in the publicly-distributed PoN generated by an earlier GATK version. We are investigating the issue and will try to solve it by producing a new Panel of Normals file with the newer version. In the mean time we recommend using Mutect2 from GATK 4.1.8.0.

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