get forward and reverse support counts for Scylla merged variants

[argoat]

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!

[tamsen]

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 BOOL Output gVCF files, 'true' or 'false'
--crushvcf BOOL To crush vcf output to one line per loci
--reportnocalls BOOL 'true' or 'false'. default, false
--reportrccounts
BOOL Report collapsed read count, When BAM files
contain X1 and X2 tags, output read counts for
duplex-stitched, duplex-nonstitched, simplex-
stitched, and simplex-nonstitched. 'true' or
'false'. default, false
--reporttscounts
BOOL Report collapsed read count by different
template strands, Conditional on ReportRcCounts,
output read counts for duplex-stitched, duplex-
nonstitched, simplex-forward-stitched, simplex-
forward-nonstitched, simplex-reverse-stitched,
simplex-reverse-nonstitched. 'true' or 'false'.
default, false
--reportsuspiciouscoveragefraction
BOOL Report fraction of total coverage (for
spanning variants, this is start + end coverage,
so up to double the reported coverage) that is
'suspicious' i.e. unanchored and bearing some
resemblance to an insertion at that site.
'true' or 'false'. default, false