I have a SAM/BAM file and instead of displaying it in IGV or another browser, I would like to make a sequence logo out of it. My favourite software WebLogo does not support SAM/BAM file as an input (instead it supports CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP)
I would like to avoid parsing SAM file by myself and adding '-' when needed. Do you have any idea if there is already some software that could do such a thing? Thanks a lot.
The second question is about different alleles. I would like to visualize sequences (reads) from each allele with another color. I have found many coloring schemes, but none dividing sequences into groups together with corresponding coloring. Thanks a lot.