search

ivanek / Gviz

This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.
https://bioconductor.org/packages/Gviz/
Artistic License 2.0
75 stars 10 forks source link

Inconsistent Indel annotation with IGV #58

Closed ctl43 closed 2 years ago

ctl43 commented 3 years ago

Hi Gviz developers, thanks for creating this powerful genome visualisation package. I used Gviz to visualise indels, however, I found that the annotation is not consistent with IGV (see figure); Gviz extended one more base to the right.

I wonder whether this is a bug or not. Here is my code read_track <- AlignmentsTrack(range = bam, stacking = "full", showIndels = TRUE, isPaired=TRUE) seq_track <- SequenceTrack(genome) plotTracks(list(seq_track, read_track), chromosome = chr, from = start, to = end) gviz_igv

Thanks!

ivanek commented 2 years ago

Hi @ctl43, Thanks for reporting. I fixed it in devel (>= 1.39.2) and release (>= 1.38.1) versions. Best, Robert