Open argoat opened 3 years ago
Hi,
Thanks for using Pisces!
Scylla will give support counts for unmerged indels (see below for various options), but as for support counts for merged complex variants, the feature does not yet exist. The read-counting strategy for phased variants is pretty murky, because Scylla merges variants by clustering, even if they are on non-overlapping reads. How to summarize that into counts gets tricky. Its certainly doable, but doing it right would take some under the hood remodeling, so we have held off getting into it so far.
best Tamsen
VCF_WRITER:
--gvcf
'true' or 'false'. default, false
Dears,
After merging neighboring INDELs and SNVs into complex indels, i don't see any information indicating forward and reverse support counts of merged variants from Scylla output .vcf file. How do i get these counts?
Thanks!