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

MateOnSameContigOrNoMappedMateReadFilter Follow

Avatar
GATK Team
  • Updated

Keep only reads whose mate maps to the same contig or is unmapped

Category Read Filters

Overview

Keep only reads that have a mate that maps to the same contig (RNEXT is "="), is single ended (not 0x1) or has an unmapped mate (0x8).

See MappedReadFilter for criteria defining an unmapped read.

Additional references

See these additional references.

Return to top

GATK version 4.1.8.1-SNAPSHOT built at Sun, 2 Aug 2020 22:56:07 -0400.

Related articles

0 comments

Please sign in to leave a comment.

Powered by Zendesk