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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NotSecondaryAlignmentReadFilter Follow

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GATK Team
  • Updated

Filter out reads representing secondary alignments

Category Read Filters

Overview

Filter out reads representing secondary alignments (0x100).

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GATK version 4.7.0.0 built at Tue, 18 Aug 2026 13:15:12 GMT.

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