Generic SNP/Indel Simulator for NGS data

[peveralldubois]

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]

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

[peveralldubois]

Hi Yilong,

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

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?

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]

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

[sirmark]

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