how to do basic statistics for bam files

Question

[adR]

Hi Bistar teams,

I have unpaired Exom-seq data. I did the quality control and alignment. Now my files are in bam format and I would like to do some basic statistics like fragment size, coverages, mismatches, Gaps , duplicates etc . May I get some tips or codes how to run it on bash/terminal?

Thank you! Best adR

[GenoMax]

qualimap (LINK).

Answer 1

[Pierre Lindenbaum]

samtools stats in.bam

[colindaven]

Yes, then follow up with

multiqc -f . &