how to do basic statistics for bam files

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

picard gatk alignment

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updated 4.7 years ago by colindaven

• written 4.7 years ago by adR

qualimap (LINK).

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written 4.7 years ago by GenoMax

1 answer

samtools stats in.bam

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written 4.7 years ago by Pierre Lindenbaum

Yes, then follow up with

multiqc -f . &

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written 4.7 years ago by colindaven

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