Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

Articles in this section

See more

MetricsReadFilter Follow

Avatar
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)

Return to top

GATK version 4.0.6.0 built at 25-39-2019 01:39:46.

0 comments

Please sign in to leave a comment.

Powered by Zendesk