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Random SNPs simulation?

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!

snp
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updated by enquiry.ticacademy • enquiry.ticacademy • written by thomasbersez thomasbersez

4 answers

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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written by jean.elbers jean.elbers

Thanks a lot! It works perfectly!

Best, Thomas

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written by thomasbersez thomasbersez

thomasbersez :

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

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written by GenoMax GenoMax

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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written by Corentin Corentin

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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written by sarahblossom1234567 • sarahblossom1234567

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