What criteria are used to determine supplementary alignment with bwa-mem (flag 2048)

Question

[annawilliford]

Greetings,

Supplementary alignment (chimeric reads, flag 2048) is set when a read aligns to 2 or more different genome locations. What is the minimum number of bases that must align to a different location to be considered a chimeric read? I have reads marked as SA when >25 bases align elsewhere, but not 8, for example. Does it depend on read length? I have bwa-mem alignments with 45-bp paired-end reads and none of the reads are set as SA reads (although I know they are), while alignments using 75-bp reads (same genome) have plenty of SA reads. BWA versions :0.7.7/0.7.12

Thank you!

Anna

[Devon Ryan]

The odds are good that you'll need to go through the code to find the answer to this. The paper describing bwa mem is only a page long, so details like this will be omitted.

[Ying W]

you could also try tagging your post bwa and hope that lh3 replies