search

anshess / SimGBS.jl

A simple method to simulate Genotyping-by-Sequencing (GBS) data.
MIT License
2 stars 1 forks source link

How to "saturate" a genome #40

Open MWSchmid opened 2 years ago

MWSchmid commented 2 years ago

Hi

I recently found your manuscript and simGBS. I was looking for a GBS read simulator because I wanted to simulate GBS data from polyploids. I.e., take different genomes, simulate reads, mix them, then do the downstream analysis. It works well so far, but what I'm somewhat missing is a way to control what fraction of the possible fragments ends up being reflected in the simulated reads. Is there a way to control this directly? I.e., to state that it should generate an average coverage of X on Y % of all available fragments.

Best,

Marc

kanji709 commented 2 years ago

Hi Marc,

Sorry, there is currently no parameter that controls the fraction of the available fragments to be simulated. However, If you're after the same set of fragments across all individuals, you could select them after the virtual digestion step. Otherwise, you could manipulate the depth matrix if you want different sets of fragments for different individuals. In the upcoming version of SimGBS, we might include the option of generating GBS reads based on a user-specified depth matrix.

Hope it helps, Jie

MWSchmid commented 2 years ago

Hi Jie

Thanks for the info. I'll keep an eye on it then.

Best,

Marc