Question: Random SNPs simulation?
1
gravatar for thomasbersez
8 days ago by
thomasbersez10
France INRA
thomasbersez10 wrote:

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 • 95 views
ADD COMMENTlink modified 8 days ago by rainadawan10 • written 8 days ago by thomasbersez10
3
gravatar for jean.elbers
8 days ago by
jean.elbers530
jean.elbers530 wrote:

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/

ADD COMMENTlink modified 8 days ago • written 8 days ago by jean.elbers530

Thanks a lot! It works perfectly!

Best, Thomas

ADD REPLYlink written 7 days ago by thomasbersez10

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

ADD REPLYlink written 7 days ago by genomax62k
2
gravatar for Corentin
8 days ago by
Corentin250
Corentin250 wrote:

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

https://github.com/price0416/Simulome

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

ADD COMMENTlink written 8 days ago by Corentin250
1
gravatar for rainadawan
8 days ago by
rainadawan10
rainadawan10 wrote:

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

ADD COMMENTlink written 8 days ago by rainadawan10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1779 users visited in the last hour