Empirical SNP data

[SarahjmRA]

Hi there,

I have genotyped ~3000 SNPs for 63 individuals, and would like to simulate future genetic variation and effective population size, under 3 different initial effective population size scenarios (250, 400 and 800). I do not know the position of the SNPs on the genome.

Is it possible to begin a simulation in GeneEvolve using empirical data, without knowledge of SNP locations?

Thank you very much.

Cheers,
Sarah

[rtahmasbi]

Hello Sarah, Definitely you can use empirical data, but check if the SNP positions belong to the recombination map (Recom.Map.b37.50KbDiff file available in Example directory). GeneEvolve needs that your data positions belongs to the recombination map. You can also download this file ftp://webdata2:[email protected]/downloads/productfiles/humanomni25exome/v1-2/infinium-omni25exome-8-v1-2-physical-and-genetic-coordinates.zip to find SNP positions. Cheers, Rasool

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On Aug 1, 2017, at 5:19 PM, SarahjmRA ***@***.***> wrote: Hi there, I have genotyped ~3000 SNPs for 63 individuals, and would like to simulate future genetic variation and effective population size, under 3 different initial effective population size scenarios (250, 400 and 800). I do not know the position of the SNPs on the genome. Is it possible to begin a simulation in GeneEvolve using empirical data, without knowledge of SNP locations? Thank you very much. Cheers, Sarah — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQ33T53hUFHcLh6nakyEMGdjUixVblcDks5sT7KZgaJpZM4OqaiC>.

[SarahjmRA]

Hi Rasool,

Thank you for your response. Sorry I should have elaborated, I am actually working with SNPs from sharks. In that case, I don't think this will be suitable for me.

Thank you anyway!

Cheers,
Sarah

[rtahmasbi]

Sarah, you can create your own recombination map with equal probabilities.

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On Aug 14, 2017, at 17:40, SarahjmRA ***@***.***> wrote: Hi Rasool, Thank you for your response. Sorry I should have elaborated, I am actually working with SNPs from sharks. In that case, I don't think this will be suitable for me. Thank you anyway! Cheers, Sarah — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQ33TxtV7NIuXOwyoU6MuuklVVxQXpG2ks5sYNrbgaJpZM4OqaiC>.