Showing docs for version 3.6-0 | The latest version is 4.1.4.0


SpanningDeletions

Fraction of reads containing spanning deletions

Category Annotation Modules

VCF Field INFO (variant-level)

Type StandardUGAnnotation

Header definition line
  • INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">

  • Overview

    The presence of many reads with deletions spanning a given site is often an indication that a variant call made at that site is in fact a false positive. This annotation counts the number of reads that contain deletions spanning the site divided by the total number of reads that cover the site.

    Caveats

    • In its current form, this annotation is not compatible with HaplotypeCaller. It is only meant to be used with UnifiedGenotyper, as its purpose is to compensate for the UnifiedGenotyper's inability to integrate SNPs and indels in the same model (unlike HaplotypeCaller).
    • By default, the UnifiedGenotyper will not call variants where the fraction of spanning deletions is above a certain threshold. This threshold can be adjusted using the `--max_deletion_fraction` argument.

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.