AlignmentAgreesWithHeaderReadFilter

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

Category Read Filters

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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 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.