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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AlignmentAgreesWithHeaderReadFilter Follow

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GATK Team

Filters out reads where the alignment does not match the contents of the header

Category Read Filters

Overview

Filter out reads where the alignment does not match the contents of the header.

The read does not match the contents of the header if:

  • It is aligned to a non-existing contig
  • It is aligned to a point after the end of the contig

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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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