input and result about combine Sweed and omega

[lwgbi...@gmail.com]

dear all：

    i am useing sweed and omega to find some selective regions in my dataset，i have some questions，thank you for your help.

    1.I have my SNPs data in a population in vcf format, can I input the vcf format SNPs directly to sweed and omega? Is the results same when the input format is vcf OR SF.In SF format, does the x=number of ALT in vcf format?

   

    2.why the posistins in sweed and omega result is decimals, what is the  different from the positons  in my vcf format? Does the positions in SweeD result same as in Omega result, they have different decimal,for example，28507.5996 and 28507.6001.

    3. how can I get the selective sweep regions from the results of Sweed and omega , in results are positions.

    

     Below is my command：

      

     RUN Omega: 

      ~/OmegaPlus_v2.3.0_Linux/OmegaPlus -name 182samples-chr3 -grid 6000 -input 182samples_genotype-orderc-chr3.vcf -minwin 100 -maxwin 10000 -seed 8564155    

     Run Sweed:

     ~/SweeD_v3.3.2_Linux/SweeD -name 182samples_chr3 -input 182samples_genotype-order-chr3.vcf  -grid 6000 –noSeparator

  And the I used the "combines the results of OmegaPlus with SweeD and detects the common outliers" pipeline to combines the results from the SweeD and Omega.

      best wishes！

      li

[N.Alachiotis]

Hi,

On Friday, August 26, 2016 at 5:28:24 AM UTC+3, lwgbi...@gmail.com wrote:

dear all：

    i am useing sweed and omega to find some selective regions in my dataset，i have some questions，thank you for your help.

    1.I have my SNPs data in a population in vcf format, can I input the vcf format SNPs directly to sweed and omega? Is the results same when the input format is vcf OR SF.In SF format, does the x=number of ALT in vcf format?

yes you can provide vcf format files to both tools. For SweeD the results are the same regardless of the input format assuming you generated the SF format using SweeD.
 

   

    2.why the posistins in sweed and omega result is decimals, what is the  different from the positons  in my vcf format? Does the positions in SweeD result same as in Omega result, they have different decimal,for example，28507.5996 and 28507.6001.

You can ignore  the  decimal parts. they are there because we internally represent the positions as floats to determine the grid locations to evaluate.

    3. how can I get the selective sweep regions from the results of Sweed and omega , in results are positions.

in OmegaPlus you can  add the -all option to see the extend of the sweep. we dont have a similar option in sweed yet.

    

     Below is my command：

      

     RUN Omega: 

      ~/OmegaPlus_v2.3.0_Linux/OmegaPlus -name 182samples-chr3 -grid 6000 -input 182samples_genotype-orderc-chr3.vcf -minwin 100 -maxwin 10000 -seed 8564155    

     Run Sweed:

     ~/SweeD_v3.3.2_Linux/SweeD -name 182samples_chr3 -input 182samples_genotype-order-chr3.vcf  -grid 6000 –noSeparator

  And the I used the "combines the results of OmegaPlus with SweeD and detects the common outliers" pipeline to combines the results from the SweeD and Omega.

      best wishes！

      li

Regards,
Nikos