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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ValidAlignmentStartReadFilter Follow

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GATK Team
  • Updated

Keep only reads with a valid alignment start

Category Read Filters

Overview

Keep only reads with a valid alignment start (POS larger than 0) or is unmapped.

See MappedReadFilter for criteria defining an unmapped read.

Additional references

See these additional references.

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

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