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AlignmentAgreesWithHeaderReadFilter

Filters out reads where the alignment does not match the contents of the header

Category Read Filters


Overview

Filter out reads where the alignment does not match the contents of the header.

The read does not match the contents of the header if:

  • It is aligned to a non-existing contig
  • It is aligned to a point after the end of the contig

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GATK version 4.1.4.0 built at Wed, 9 Oct 2019 15:19:59 -0400.