Discrepancy in Total Counts Displayed at the Same Position in IGV and IGV.js for the Same BAM File
zongzi111 opened this issue · 6 comments
I have encountered a discrepancy in the total counts displayed for the same genomic position in both the desktop version of IGV and IGV.js when working with the same BAM file.
I haven't been able to reproduce this. Can you share a small test case?
Is it possible you have disabled filters in igv-desktop, such as "vendor failed" or "duplicates"?
It's possible that I may have disabled some filters in IGV-desktop, but please note that the settings in IGV-desktop are at their default values. I'm interested in ensuring that the results in IGV.js match those of the desktop version consistently. Below is a specific case to illustrate the issue:
https://drive.google.com/drive/folders/16tbMR_aDmfV29azhhQm2032tlTTyjzI_?usp=sharing
locus：chr7:140,739,907-140,739,947
If there are specific steps or configurations I need to follow in IGV.js to achieve results consistent with IGV-desktop, please let me know. I would appreciate any guidance or recommendations to address this inconsistency.
How have you confirmed that the settings in IGV-desktop are at their default values? I get exactly the same counts between IGV desktop & igv.js, see the screenshot. To insure you are at default values first shutdown IGV, then delete or rename prefs.properties in the igv folder, then restart. Also, you didn't say what version of IGV or igv.js you are using, I am assuming recent versions of each.
Filter duplicate reads affect this value, I was wondering how to turn off this filter in igv.js.
I have found how to disable this filter by adding filter: {duplicates: false} in the track configuration. Thank you.