Question: Filter bam, EXCLUDING specific tagged reads

gravatar for dayne.filer

13 hours ago by

I am trying to use samtools view to filter a bam file. I would ideally like to take a sorted bam with the DT flags set by picard markduplicates (e.g. DT:Z:SQ for optical/sequencing and DT:Z:LB for PCR/library) and exclude reads with either DT:SQ only OR DT:SQ & DT:LB. As far as I can tell, samtools only supports filtering by including specific tag:value pairs with the -d parameter. Is there any workaround here? Or is the only option to write another intermediate file?

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