Per base statistics on an RNAseq bam file

Question

[tassa.saldi]

Hello,

Does anyone know how I can create a file that gives me coverage, mismatches, insertions and deletions from an RNAseq bam file? Pysamstats is not working as it counts spliced regions as deletions and the spliced region is also added to the coverage (both incorrect). I also cannot split the reads with Bedtools first because they are split on both the N CIGAR (spliced) and the D CIGAR (real deletions). Basically I need the information you get from hovering your curser over a position in IGV in a tab file.

Thanks in advance!

[GenoMax]

Check out bam-readcount.

[WouterDeCoster]

Cross-posted to SeqAnswers