Can I use Delly2 to call SV from Whole-Exome sequencing data?

[Qingrun ZHANG]

Can I use Delly2 to call SV from Whole-Exome sequencing data? I tried it on my mouse WES data. Some the result show supper huge deletions with size 13.6Mb. I understand it is from tumor sample, but I am not sure whether we are able to see such huge deletion just from WES data. Also the median deletion size is quite similar across samples, no matter it is normal sample or tumor sample. I am not pretty sure whether it is reasonable. Thanks for any advise!

Qingrun

[Tobias Rausch]

We haven't used Delly a lot on WES data. The problem is that you often have a very tight insert size distribution and thus, not much power using paired-end mapping. Have you tried already `delly filter -f somatic ...` ? At least the new small InDels <500bp may work using WES data.

Best, Tobias

On Tue, Jun 28, 2016 at 6:57 PM, Qingrun ZHANG <zha...@gmail.com> wrote:

Can I use Delly2 to call SV from Whole-Exome sequencing data? I tried it on my mouse WES data. Some the result show supper huge deletions with size 13.6Mb. I understand it is from tumor sample, but I am not sure whether we are able to see such huge deletion just from WES data. Also the median deletion size is quite similar across samples, no matter it is normal sample or tumor sample. I am not pretty sure whether it is reasonable. Thanks for any advise!

Qingrun

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