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-   -   Generic SNP/Indel Simulator for NGS data (http://seqanswers.com/forums/showthread.php?t=8847)

peveralldubois 01-13-2011 01:41 AM

Generic SNP/Indel Simulator for NGS data
 
Expert is there any existing SNP/Indel Simulator for NGS reads?

The principle the tool does something like taking any reference genome, pick positions randomly in that genome and begin to introduce SNP or indels in that position. Finally the tool should give reads given from the variant genome above with certain depth, and location of SNP/Indel is introduced in the reads fasta header.

Yilong Li 01-13-2011 03:47 AM

I think Maq does that, you should take a look at http://maq.sourceforge.net/maq-manpage.shtml#7

peveralldubois 01-13-2011 05:54 AM

Hi Yilong,

Thanks so much for your reply.
I tried to run 'fakemut' from maq using this command.

Code:

maq fakemut chr22.fa > out.fakeref.fasta 2> out.fake.snp
Do you know what does each column means from "out.fake.snp"?
I can guess, but I am not quite sure.

I can't seem find any explanation about it from the web?

Code:

chr22  16051056        G      c      99
chr22  16054178        -      T      99
chr22  16055216        C      G      99
chr22  16056830        A      C      99
chr22  16056930        A      G      99
chr22  16057491        G      A      99
chr22  16058778        C      t      99


drio 01-13-2011 05:59 AM

Also take a look to dnaa, specifically the dwgsim (forked from the maq tool).

sirmark 05-02-2013 05:12 AM

I need to generate a small dataset of individuals organized in pool... with SNP and indel
is there a way to do this ?


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