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!
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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