Exome Sequencing: Large Indel

Question

[Sara]

Hi everone,

How can we detect large indels ( more than 25 bp) in exome sequence data?

Any references?

Thanks Sara

[Travis]

Different technologies mean different read lengths which mean different approaches to problem solving.

[Travis]

What sequencing technology? Are you using single or paired-end data?

[Hranjeev]

Noob here in HT sequencing. May I know what the sequencing technology have to do with it?

Answer 1

[Sean Davis]

Have a look at this nice site: http://bioops.info/2011/02/software-packages-for-discovering-structural-variation-with-next-generation-sequencing/

Answer 2

[Vitis]

A somewhat unconventional approach, first de novo assembly then align the contigs to detect the indels. The candidates can be verified by read mapping. This would miss some true indels, but I'd expect less false positives.