Dear Broad Institute,
Utilizing igv and igvtools, we were able to create a wig file using a bam file. However, if we want to be able to calculate the sum of mismatch qualities, is there a way to extract this information from a .wig file using igvtools to calculate the sum of mismatched base qualities and sum of all qualities? If not, what file should I convert the bam files to in order to successfully obtain the sum of mismatched base qualities and sum of all qualities?
Thank you so much,
Justin Zhu