Re: [svtoolkit-help] GenomeSTRIP

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

It has been used with some success on non-human diploid organisms.

But am I right that p. falciparum is haploid?
That might actually be ok for the most part, but would require you to 
change some settings and look carefully at the results.
If you're motivated and have good informatics skills I think it should 
be doable.

I think you could set the diploid and haploid genome sizes in the 
configuration file to the same values, as a first step.
You would also want to override the default filtering.
In discovery, you would want to not use the membership test, since that 
assumes a diploid organism, but this filter is not very important.
In genotyping, you would want to not use the inbreeding coefficient 
filter for the same reason.

To do GC-bias correction, which is very useful, we currently use a mask 
to remove regions that may not be fixed ploidy in all samples.
This doesn't have to be perfect, but it is good to remove known 
copy-number-polymorphic regions.
Worst case, I might suggest masking nothing and doing gc-bias correction 
anyway (or trying with and without and seeing which way gives you
tighter clusters in genotyping).

So, it might be a bit of an adventure.  But if you run into places where 
the code is assuming diploid, I can look into fixes for you.
The good news is that it's a small genome, so the computational burden 
won't be so large, and homozygous deletions are much easier to detect.

-Bob

On 1/9/13 1:11 PM, Harold Ocholla wrote:
> Hello,
>
> Can I use GenomeSTRIP to analyse non human data, for example plasmodium falciparum?
>
> Regards, Harold.
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