Re: [svtoolkit-help] high depth region

[Bob H. <han...@br...>]

This is a known problem.
One solution is to run the parallelism more fine-grained (this is 
usually what I do).
Another solution is to simply not run these regions (notably the 
peri-centromeric regions on chr10 and chr2).
You can control this with -L.
You are unlikely to get good calls in these regions.
There is currently no other way to throttle back processing in these 
regions, although I agree it would be useful.
-Bob

On 4/4/12 5:19 PM, Ashish Kumar wrote:
>
> Hi Bob,
>
> While trying to run discovery pipeline over the whole-genome, there 
> are certain regions that are high depth region (and presumably very 
> low complexity).
>
> For eg. on a chr10's 2Mb region, the discovery is able to complete 
> only about 20% of the region in 3 days of computation.
>
> Shall I parallelise this region further into smaller discovery regions 
> or there are other ways that GenomeSTRiP can cope up with in such a 
> situation?
>
> Thanks,
>
> Ashish
>
>
>
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