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Random SNPs simulation?
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18 months ago
thomasbersez • 30
France INRA

Hi everyone,

For an allele mining project I need to generate in silico NGS data. I have chosen to use Grinder to do so. I would like to add randomly generated SNPs to my reference genome, is any software available to do that ?

Thanks for help!

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13 months ago
jean.elbers ♦ 1.1k

You could try mutate.sh from BBTools/BBMap. mutate.sh can also produce a VCF file of the SNPs added. You can also generate random Illumina reads with the BBTool randomreads.sh https://sourceforge.net/projects/bbmap/

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13 months ago
Corentin • 290

Hi, you can also try Simulome, it is quite customisable.

https://github.com/price0416/Simulome

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870732/

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17 months ago
rainadawan • 10

To evaluate statistical methods for genome-wide genetic analyses, one needs to be able to simulate realistic genotypes. We here describe a method, applicable to a broad range of association study designs, that can simulate autosome-wide single-nucleotide polymorphism data with realistic linkage disequilibrium and with spiked in, user-specified, single or multi-SNP causal effects. https://www.gangboard.com/cloud-computing-training/aws-training

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14 months ago

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14 days ago
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