Question: simulating illumina data with spiked variants
1
gravatar for Richard
3.3 years ago by
Richard500
Canada
Richard500 wrote:

Hi all,

I am looking to simulate some paired illumina data for a test.   What I want to do in order of importance (most important at the top)

  1. Create fastq files.
  2. Specificy specific SNPs to be in the data
  3. Control the allelic fractions of the spiked in SNPs
  4. Have an appropriate error model of illumina sequencing
  5. Have controllable metrics like duplicate rate, chastity fail rate

There seem to be a number of tools available for simulating illumina - do we know of one that can handle my requirements?

 

 

simulated data illumina • 978 views
ADD COMMENTlink modified 7 weeks ago by Gabriel R.2.1k • written 3.3 years ago by Richard500
2
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan71k
Freiburg, Germany
Devon Ryan71k wrote:

Aside from #5, any of the common simulators (wgsim, Sherman, etc.) can do that. For the SNPs, just make a second genome containing them, sample from that as well, and then mix the results in the fraction that you'd like.

ADD COMMENTlink written 3.3 years ago by Devon Ryan71k

I checked both wgsim and sherman and I didn't see a way to spike in specific variants (base change and position). Am I missing something?

ADD REPLYlink written 3.3 years ago by Richard500
1

Read the entirety of my answer, I mentioned the variants explicitly.

ADD REPLYlink written 3.3 years ago by Devon Ryan71k
0
gravatar for Gabriel R.
7 weeks ago by
Gabriel R.2.1k
Center for Geogenetik Københavns Universitet
Gabriel R.2.1k wrote:

For 1, 2 (maybe 3), 4 we developed a sequencing simulator for ancient DNA: grenaud.github.io/gargammel/ But it can be used to simulate modern DNA. For the PhiX, you can add it as a "microbial contaminant". It automates the process of fragment size distribution, sampling from a diploid genome and generate Illumina-like fastq files. Just give it a "diploid" genome represented by 2 fasta files.

ADD COMMENTlink written 7 weeks ago by Gabriel R.2.1k
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