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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Is there a way to filter the modified bam based on q score? #916

Open yinyuanmtu opened 2 days ago

yinyuanmtu commented 2 days ago

I have used dorado base called the data without --min-qscore . I am now trying to filter the bam file (with base modifications) based on q score. Is there a way to do that, or I have to re-base call including --min-qscore. Thanks!

HalfPhoton commented 2 hours ago

Please take a look at https://www.htslib.org/doc/samtools-view.html which has some filtering options. Similarly you can write some simple python scripts using pySam.

Kind regards, Rich