Open lindenb opened 3 years ago
I'll get a fix for this in next release. Meanwhile, the solution is just to drop them. can do this with slivar with someting like:
slivar expr --pass-only --info "variant.start <= variant.stop" -v $input -o $output
Just following up here to see if this has been resolved in the latest release (0.2.8) as I am not seeing it detailed in the release notes...
no. not fixed. by next release, I mean, next release. ;) meanwhile, I would just add a step to remove these variants as they are low quality anyway.
Hi,
FYI, when using /smoove-0.2.6 + singularity. With
smoove genotype
, some variants have POS>INFO/END.command:
log:
example:
the variant was already present in the 'merge' vcf: