Do you know how can I filter out supplementary alignments from a bam file? I was reviewing broadinstitute.github.io/picard/explain-flags.html and I am aware that the flag for this kind of alignments is "2048". However, depending on another features (ex: paired read, second in pair, etc), the flag can vary.

So, I am not sure about how can I filter out this kind of alignments.

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