Hi!

Do you know how can I filter out supplementary alignments from a bam file? I was reviewing http://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.
`samtools view -F 2048 -bo filtered.bam original.bam`

You don't have to care about what other flags are set, the `-F` option will filter any entry with bit 2048.