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Old 01-20-2022, 08:14 AM   #1
akoontz11
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Question 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!
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File Type: zip QUAC_filtered_algnSummary.zip (14.9 KB, 0 views)

Last edited by akoontz11; 01-20-2022 at 08:19 AM. Reason: Adding attachment
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Old 01-20-2022, 08:23 AM   #2
akoontz11
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Default 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In going through my own post, I've realized that the issue may simply be I'm running an outdated version of samtools...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.
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