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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MateOnSameContigOrNoMappedMateReadFilter Follow

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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.

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GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.

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