I am currently performing an analysis on pancan TCGA wxs data (>10000 normal-tumor pairs) . For my analysis I need to have the total coverage of each BAM file, so I can perform a depth normalization for on tumor vs matched normal sample.
Does anyone know where can I get total read number without downloading ~10000 samples BAM files?
My initial idea was to find the .bam.bai files and use them to find the total number of reads, but I couldn't find those files either.
Appreciate your help, Thanks