To Simulate Heterozygous Variations In Genome

Question

[Pascal]

A bit technical question here... I want to simulate an heterozygous indel starting from a piece of reference genome (FASTA file) and I thought about the following workflow to do it. Could you comment it? Is it a good idea or is there a better approach?

1. copy of reference file (let's call it ref.fasta) to ref_insert.fasta

2. edit ref_insert.fasta and insert a sequence of 10bp for instance,

3. concatenate both fasta files ref.fasta into a new fasta file (ref_diploid.fasta)

4. simulate short reads with a simulator (my favorite one is wgsim) disabling mutations generator,

5. align and then detect variants.

Answer 1

[Stefano Berri]

You can start this way, but then I would leave the mutation generation on (your sample will never be exactly like the reference genome). Also, you can insert a few of different size and/or in random locations, so that you get an idea of how likely it is to pick it up.

[Pascal]

Of course, you're right. Good point, thank you Stefano.

Answer 2

[Attila Berces]

At Omixon we developed tools for simulating reads with various mutations. The input is a multi-fasta reference file and a VCF file. It can simulate Illumina and Ion Torrent reads with specified length and distance in case of paired data. We offer it next month as a free on-line service, but if you do not want to wait we can give you a command line version for personal use. you can fill the contact form on www.omixon.com.