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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GATK Team

Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments

Category Read Filters

Overview

Filter out reads that:
  • Fail platform/vendor quality checks (0x200)
  • Are unmapped (0x4)
  • Represent secondary/supplementary alignments (0x100 or 0x800)

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GATK version 4.1.9.0-SNAPSHOT built at Mon, 19 Oct 2020 11:41:12 -0400.

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