How do people query paired-end data?

[derobins]

Hi all,

I have a couple of questions about how people query their paired-end data. I am a software engineer and not a direct consumer of NGS data, so please forgive my naivete.

1) What sort of questions do people tend to ask of the data? I can conceive of simple queries such as "What unexpected size variation exists in a file or region?" but I'm sure there are more complicated ways to interrogate the data.

2) Is the way that SAM/BAM stores paired end information suitable for these queries? If not, how could it be improved?

Thanks,

Dana Robinson
The HDF Group