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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SecondOfPairReadFilter Follow

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GATK Team

Keep only paired reads that are second of pair

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Overview

Keep only paired reads (0x1) that are second of pair (0x80).

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GATK version 4.2.1.0-1-gf548ccd-SNAPSHOT built at Mon, 2 Aug 2021 14:22:45 -0700.

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