Documentation

SpanningDeletions

Fraction of reads containing spanning deletions

Category Variant Annotations

VCF Field INFO (variant-level)

Type StandardAnnotation

Header info
  • INFO=

  • 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

    • This annotation is not compatible with HaplotypeCaller; 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.

    Return to top


    See also Guide Index | Tool Documentation Index | Support Forum

    GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA