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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NotProperlyPairedReadFilter Follow

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GATK Team

Keep only paired reads that are not properly paired

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Overview

Keep only paired reads that are marked as not properly paired (0x1 and !0x2). Removes unpaired reads.

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GATK version 4.1.5.0-SNAPSHOT built at Wed, 4 Mar 2020 13:47:07 -0500.

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