SAM flags meaning

Question

[lilach.kornblitno]

Hi all,

I'm struggling with finding explanations to the SAM flags presented on my sam file. to clarify, I am familiar with the picard tool in which one can find the meaning, only it is written very briefly and i don't know what it means de facto?

i.e I know flag No. 99 means in summary: read paired, read mapped in proper pair, mate reverse strand, first in pair. I don't understand what does "mate reverse strand" or "first in pair" mean? what read qualifies to this definition? what criteria checked?

Does anyone know a file that explains the flags with more details other than the picard tool and the Format Specification?

Thanks!

Answer 1

[Pierre Lindenbaum]

for an illustration see http://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/

or my presentation, starting from slide #32 http://www.slideshare.net/lindenb/ngsformats?ref=http://plindenbaum.blogspot.com/2013/09/presentation-file-formats-for-next.html?m=1 (update 2024: i deleted my slideshare account)

[lilach.kornblitno]

Thank you very much! this is exactly what I was looking for. Is this taken from any formal SAM documentation or are these your conclusions from working on different SAM files?

And one more thing, if I may, do you know how is it possible for a read to get both "first in pair" and "second in pair if the flag also means "read mapped in proper pair"? (i.e see Picard tool explanation for flags 195, 211, 227 or 243)

[-_-]

For fast and handy interpretation of the flag, try http://www.samformat.info/#/flag

[Susmita Mandal]

I am understanding the SAM flags to some extent. But I have a paired end data and I have mapped it to a reference genome and I would like to split that BAM file into plus and minus strands w.r.t. reference genome. So i don't understand how to go about it. Please help me.