Question

how to do basic statistics for bam files

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2.5 years ago

adR ▴ 120

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 • 840 views

ADD COMMENT • link updated 2.5 years ago by colindaven 6.4k • written 2.5 years ago by adR ▴ 120

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qualimap (LINK).

ADD REPLY • link 2.5 years ago by GenoMax 142k

score 2 · Accepted Answer · 2021-12-06

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2.5 years ago

Pierre Lindenbaum 161k

samtools stats in.bam

ADD COMMENT • link 2.5 years ago by Pierre Lindenbaum 161k

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Yes, then follow up with

multiqc -f . &

ADD REPLY • link 2.5 years ago by colindaven 6.4k