Fraction of reads containing spanning deletions
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.
- 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
Guide Index |
Tool Documentation Index |
GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51.