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When used with --zoom option, samplot's genome coordinates in the x-axis are incorrect. The plot itself appears to be correct and the only problem appears to be with the x-axis coordinates not lining up.
This is demonstrated here using an example deletion call chr1:58343207-58343542 using test dataset from this repo "test/data/hg19_chr1_58343117_58343622_deletion.bam". Note that in the zoom mode, start and stop coordinates do not line up with SV call itself, unlike in normal samplot mode (ie. without --zoom) and IGV.
When used with
--zoom
option, samplot's genome coordinates in the x-axis are incorrect. The plot itself appears to be correct and the only problem appears to be with the x-axis coordinates not lining up.This is demonstrated here using an example deletion call
chr1:58343207-58343542
using test dataset from this repo"test/data/hg19_chr1_58343117_58343622_deletion.bam"
. Note that in the zoom mode, start and stop coordinates do not line up with SV call itself, unlike in normal samplot mode (ie. without--zoom
) and IGV.Normal mode:
Zoom mode:
IGV view:
Script:
I tested this using samplot versions
1.1.0
and1.3.0
, but this bug has been present since--zoom
feature was introduced.The text was updated successfully, but these errors were encountered: