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 unmapped reads

Category Read Filters

Overview

Filter out unmapped reads.

Unmapped reads are defined by three criteria:

  • SAM flag value 0x4
  • An asterisk for reference name or RNAME (column 3 of a SAM record)
  • A zero value for leftmost mapping position for POS (column 4 of SAM record)

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GATK version 4.4.0.0 built at Thu, 16 Mar 2023 15:00:37 -0400.

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