Question about sort by base option

[Thomas Ward]

Hello, I have a question about the sorting by base option. I'm using version 2.16.2 and when I sort by base, it will bring the alleles with lowest VAF to the top above the highest VAF allele, including reads with soft clipped bases. Is there a way I can reverse this order and have the highest VAF allele at the top when sorting? This was how it used to be previously. 

Thanks

[igv-help]

I'm not sure I understand the question,  perhaps a screenshot would help.   I will assume you are asking about IGV desktop.    Sorting brings reads that mismatch the reference at the center line to the top.   Reads with a deletion at the centerline, if any, come next.  Finally reads that match the reference at the centerline.    If there are multiple bases mismatching the reference they are sorted lexigraphically.   There is no concept of "VAF" in this sort.     This is what I see at a site with multiple mismatches.  

[Thomas Ward]

Thanks for the reply and yes, I'm talking about IGV desktop. The first screenshot is from version 2.11.2, where at a deletion location the deletion reads sort to the top first (due to it being the most prominent mutation at this location), followed by the mismatch reads. The second screenshot is the same location, again filtered by base, in version 2.16.2 and it filters using the rules that you described. I was wondering if there was a way that I could have the "sort by base" function revert back to the rules used in version 2.11.2, where the reads with the most prominent mutation will sort to the top.

Thanks

Tommy

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[igv-help]

There are no options for sorting currently.   I can't speak with any confidence on what release 2.11 did,  but a sort as you described would be complicated to implement.