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Old 03-22-2013, 08:51 AM   #1
nh3
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Default reads simulator?

I'd like to simulate reads from a genome with certain specified point mutations relative to the human reference. Is there a simulator that takes both a ref and a list of variants, say in vcf format? It seems that most simulators are able to generate random variants instead of specified variants.

Alternatively, are there tools to generate 'mutant' fasta files by merging a reference with a list of variants?

Any advice is appreciated.
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Old 03-22-2013, 01:03 PM   #2
BAMseek
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You might want to check out dwgsim by Nils Homer. It allows you to specify a reference and a list of mutations (-m for text format or -v for vcf).

Justin
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Old 03-22-2013, 02:42 PM   #3
nh3
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Quote:
Originally Posted by BAMseek View Post
You might want to check out dwgsim by Nils Homer. It allows you to specify a reference and a list of mutations (-m for text format or -v for vcf).

Justin
Thank you! I'll have a look at it.
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