Split Reads vs Supplementary Reads

Question

[ARB]

Hi Guys,

I am wondering what makes an alignment supplementary. I have read Samtools spec and couple other posts but it isn't that clear to me. My question is that I know Supplementary reads are chimeric alignments that align somewhere else, but then how do they differ from split reads?

My understanding is split reads can have overlaps but supplementary reads don't have "large" overlaps. Is this correct?

Thank you so much for your help.

Ashini

[stolarek.ir]

split read is a conceptual name for the situation, that your read is broken in 2 parts. And to say it is a split read you have a bit wise flag of 0x800 marking supplementary alignment. It's a naming thing (another name for this is a chimeric read). It links with the fact, that 0x800 flag was added later than built in ability for aligners to find split-reads, and some software which didn't have implemnted this supplementary read flag give a flag of 0x100, marking that the read wasn't linear, but not saying was it true supplementary (true split read) or not. So just a naming in this case

[ARB]

Thank you so much @stolarek.ir This is very helpful. So, ideally all supplementary reads are split reads only.

Thanks.