Samtools: remove unmapped reads as well as reads that are mapped incorrectly
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11 months ago

Hello, I have to remove unmapped reads and mapped incorrectly reads by using samtools view. I have found in the internet and in samtools view manual, to do that I have to use options -F and -q. But I don't understand how people decide to use, for example, -F 4 -q 10 or -F 8 and so on. On what I have to base on, then I want to chose "power" of options?

samtools • 293 views
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