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

MateDifferentStrandReadFilter Follow

Avatar
GATK Team
  • Updated

Keep only reads with mates mapped on the different strand

Category Read Filters

Overview

For paired reads (0x1), keep only reads that are mapped, have a mate that is mapped (read is not 0x8), and both the read and its mate are on different strands (when read is 0x20, it is not 0x10), as is the typical case.

See MappedReadFilter for criteria defining an mapped read.

Additional references

See these additional references.

Return to top

GATK version 4.2.0.0-SNAPSHOT built at Mon, 22 Feb 2021 13:44:49 -0800.

0 comments

Please sign in to leave a comment.

Powered by Zendesk