[Howto]Build Simulated Dataset Of Pooled Samples With Snp&Indel
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9.6 years ago
marcodpc ▴ 60

I want to generate a simulated dataset of pooled diploid individuals, with SNP and indel, to make a comparison of SNP and INDEL calling software actually available like: GATK, samtools, varscan and others.

How can I do it ?

thanks for support!

dataset human • 2.5k views
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9.5 years ago
Tky ★ 1.0k

You can use Maq to generate fake mutations/indels at given frequency based on a reference sequence (hg19 or mm9)

You may refer the fakemut command here. Furthermore, Maq can also generate stimulated short read sequences.

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9.5 years ago
cts ★ 1.7k

There are a number of read simulators out there, I've used grinder, and mason (but there are many more). I'm not sure if they explicitly give you diploid simulations...

A quick search on github gave me these two results:

https://github.com/jstjohn/SimSeq

https://github.com/lh3/wgsim

both of which mention diploid genomes in their README files, haven't tried them though

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Hey how did you install Grinder? I am unable to do so, this may be due to my insufficient shell scripting language. I understand the usage of Grinder but not able to use it. I am relatively new to the field of metagenomics. Thanks

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check out the website on sourceforge (http://sourceforge.net/projects/biogrinder/files/?source=navbar) particularly the installation section

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