[Howto]Build Simulated Dataset Of Pooled Samples With Snp&Indel

Question

[marcodpc]

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!

Answer 1

[Tky]

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.

Answer 2

[cts]

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

[meghnav89]

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

[cts]

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