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samtools v1.7 flagstat tsv output formats

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  • samtools v1.7 flagstat tsv output formats

    I'm using samtools v1.7 flagstat command to summarize a reference alignment I've performed using paired-end data. I understand the output alright (attached), but I want this data in a table format (like tsv) to share it and summarize results.

    But according to the samtools v1.7 manual, there are no output options for flagstat--is that correct? I'm surprised because v1.14 looks it has a tsv output format (-O tsv), which would solve my problem. But using that argument causes my more recent version of flagstat to fail...

    I appreciate any feedback if others have encountered/gotten around this. Thanks!
    Attached Files
    Last edited by akoontz11; 01-20-2022, 09:19 AM. Reason: Adding attachment

  • #2
    Update: samtools v1.7 flagstat tsv output formats

    In going through my own post, I've realized that the issue may simply be I'm running an outdated version of samtools... I'm updating and retying the flagstat command now.