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 ?
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.shhttps://sourceforge.net/projects/bbmap/
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.
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