Does sam 2048 flag discriminate secondary from supplementary alignments?

Question

[resug]

Hi all,

Do you know if the 2048 flag of 'samtools view -F' would also remove secondary alignments? I know that the flag 2048 is for supplementary alignments and 256 is for secondary alignments, but I am wondering if 2048 would also count secondary alignments since it is the same read aligned to a different location. Thanks.

Answer 1

[GenoMax]

2304 should cover both. See: https://broadinstitute.github.io/picard/explain-flags.html

[resug]

That makes sense. Thank you.

Answer 2

[aw7]

No, they are different things. Secondary alignments are usually alternatives to the primary alignment. Supplemental alignments are usually fragments of a read that align to a different place.

As GenoMax says, 2034 should cover both options.

[resug]

That answers my question. Although I believe you meant 2304, not 2034. Thank you.