how to do basic statistics for bam files
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5 months ago
adR ▴ 100

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 • 360 views
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qualimap (LINK).

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5 months ago

samtools stats in.bam

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Yes, then follow up with

multiqc -f . &
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