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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ProperlyPairedReadFilter Follow

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GATK Team

Keep only reads that are properly paired

Category Read Filters

Overview

Keep only paired reads that are properly paired (0x1 and 0x2). Removes single ended reads.

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GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.

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