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Exome Sequencing: Large Indel

Hi everone,

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

Any references?

Thanks Sara

exome
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updated by Biostar Biostar • written by Sara • Sara

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

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written by Travis Travis

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

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written by Hranjeev Hranjeev

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

• 222 views • link
written by Travis Travis

Different technologies mean different read lengths / protocols which mean different approaches to problem solving

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written by Travis Travis

2 answers

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

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updated by Ram Ram • written by Sean Davis Sean Davis

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.

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written by Vitis Vitis

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