# SpanningDeletions

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

• 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.