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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NotProperlyPairedReadFilter Follow

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GATK Team
  • Updated

Keep only paired reads that are not properly paired

Category Read Filters

Overview

Keep only paired reads that are marked as not properly paired (0x1 and !0x2). Removes unpaired reads.

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

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    fanfan

    I want to use the tools NotProperlyPairedReadFilter ,and I don't find the usage .So  I try to run it by the regular way (./gatk  NotProperlyPairedReadFilter ,output A USER ERROR has occurred: 'NotProperlyPairedReadFilter' is not a valid command) ,so can you give me an example to use it ,Thankyou very much. 

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