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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NonZeroReferenceLengthAlignmentReadFilter Follow

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GATK Team
  • Updated

Filter out reads that do not align to the reference

Category Read Filters

Overview

Filter out reads that do not align to the reference. Filter interprets each of the CIGAR operators M, D, N, = and X as alignment.

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

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