[BioC] Visualization of alignments with mismatch bases

[Julian Gehring]

Hi Tengfei,

What you describe covers what I tried to do so far (overlapping tracks, 
really a hacky task).  Having these modes would be very handy to have, 
especially in combination with the other capabilities of 'ggbio'.  All 
the three modes would be good to have; I would consider (1) the most 
useful one for me at the moment.  The more detail to incorporate in the 
alignments (e.g. including SNV information of a VCF file) would need 
additional relations between BAM alignments and the VCF.

I am not aware of any R package with this functionality, but I see a 
large potential for this.  Currently, I interact with IGV using batch 
mode, but this far away from being a good and long-term solution.

Best wishes
Julian


> You are right, currently ggbio only supports summary of mismatch showing
> as coverage plot and barchart(?stat_mismatch), but looks like what you
> want is detailed short reads alignments visualization with mismatch
> bases showing right on the reads, . It's possible, but not easy to do it
> manually...you have to have two GRanges objects, one for alignment one
> for SNP, and plot them layer by layer, the tricky part is assigning each
> reads fixed stepping level, so snp can be plotted on the right position.
> I will NOT recommend you to do this, it's probably not worth taking time
> doing it. I need to implement this features in some easy way.
>
> The tricky part is that there are different modes, 1. show reads as gray
> rectangle, and color mismatch as segment  2. show SNP as nucleotide
> text, A/C/T/G..,  3. show sequence detail for each alignment. those
> depends on zoomed level and even coverage, and I guess most time you
> don't want to see bases for every reads...
>
> Just curious for future ggbio development, are those modes want you
> want?  are you just using bam files here? no VCF files involved right?
> Because you mentioned 'snp', I think what you mean is mismatch?
>
> ps:  I cannot speak for other tools, and only thing I know, in SRAdb
> package, looks like it could fire your data in IGV..
>
> Thanks
>
> Tengfei
>