What is the Position in SweeD and OmegaPlus report files ?

[weikai...@gmail.com]

Hi Omegaplus supports,

I got the OmegaPlus and SweeD report files, and got the outliers by simulation. But I can not understand the positions in report file. I do not know the position is only a specific point or is start point of regions. So I don't know how to get a position information in the genomes from report file.

Best,

Kai

[Nikolaos Alachiotis]

The positions are specific points in the genome. Due to the grid size, you might notice consecutive positions yielding the same score. You can consider this a region since nothing has changed in the neighboring SNPs, thus giving the same score.

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Nikolaos Alachiotis

[weikai...@gmail.com]

Thanks for your reply. So, if the position just a specific points in the genome and this point is not a snp, how to annotate it ? 

在 2019年3月20日星期三 UTC+1上午11:34:50，N.Alachiotis写道：

[weikai...@gmail.com]

Hi,

Thanks again. Another question is which regions were calculated on this specific point, for example left or right 10KB region of  this point. I know omegaplus have -minwin and maxwin. But SweeD don't have any parameters to set it. 

在 2019年3月20日星期三 UTC+1上午11:34:50，N.Alachiotis写道：

The positions are specific points in the genome. Due to the grid size, you might notice consecutive positions yielding the same score. You can consider this a region since nothing has changed in the neighboring SNPs, thus giving the same score.

[Nikolaos Alachiotis]

Both SweeD and OmegaPlus operate in a similar way evaluating multiple SNP windows around the reported location.

SweeD implements a different criterion for the extent of this search per reported location, one that doesnot require a parameter. It reports the region however, similarly to OmegaPlus. This is implemented in SweeD version 3.3.5.

Nikos

[weikai...@gmail.com]

So, if Omegaplus can also output start position and end position like SweeD ?

在 2019年3月21日星期四 UTC+1下午4:58:58，N.Alachiotis写道：

[Nikolaos Alachiotis]

Yes both OmegaPlus and SweeD do that. But only the latest version of SweeD.

[weikai...@gmail.com]

So, the report file of omegaplus don't print start_position and end_position ?

在 2019年3月22日星期五 UTC+1上午11:09:01，N.Alachiotis写道：

[Nikolaos Alachiotis]

Yes it does. You need to include the -all command-line flag.