hammerlab
summary visualization across many BAMs
We are hitting situations where we have multiple BAMs for an individual (say 5 - 20), and are interested in looking at a summary of the read evidence at particular loci (usually loci where a variant has been called in some sample). Currently, the way I've been doing this is with a python script that outputs a PDF with many rows (one for each variant) like this:
On the far left, there are the alleles (first is reference, second is alternate, then the remaining alleles in order of number of reads supporting them), then a description of the variant (locus, gene, effect), then pie charts showing for each sample the fraction of reads supporting each allele.
I haven't done this enough yet to know if these charts are really the best way of looking at this data, but I think it'd be useful to start thinking about how this information could be conveyed in a more interactive form in CycleDash.
