ngsSim

Program to simulate NGS data for up to 3 populations. It allows for variable error rates, sequencing depth, variability, base frequencies, individual inbreeding coefficients or Fst. It outputs true genotypes, reads and genotype likelihoods.

It appears that the newest version of ANGSD does not entirely support ngsSim output anymore, unless you specify the reference sequence using -fai option. A valid alternative to simulate NGS data that can be then processed with ANGSD and ngsTools is MsToGlf.

Installation

ngsSim can be easily installed but has some external dependencies:

• Mandatory:
  • gcc: >= 4.9.2 tested on Debian 7.8 (wheezy)
  • zlib: v1.2.7 tested on Debian 7.8 (wheezy)
• Optional (only needed for testing or auxilliary scripts):
  • md5sum
  • samtools

To install the entire package just download the source code:

% git clone https://github.com/mfumagalli/ngsSim.git

and run:

% cd ngsSim
% make

To run the tests:

% make test

Executables are built in the main directory. If you wish to clean all binaries and intermediate files:

% make clean

Usage

Example:

% ./ngsSim/ngsSim -outfiles pop -npop 2 -nind 20 20 -nsites 100000 -depth 4 -pvar 0.10 -F 0.3 0.3

Parameters:

• -outfiles CHAR: Prefix for output files
• -npop INT: Number of populations. This MUST be set before -nind [1]
• -nind INT: Number of diploid individuals for each population [10]
• -nsites INT: Number of sites [500000]
• -errate FLOAT: The sequencing error rate [0.0075]
• -depth INT or FILE: sequencing depth OR file with individual depths per line [5]
• -pvar FLOAT: Probability that a site is variable in the population [0.015]
• -mfreq FLOAT: Minimum population frequency [0.0005]
• -F FLOAT [FLOAT]: FST value of 1st and 2nd split [0.4 0.1] OR inbreeding value/file in case of 1 pop [0], if 2 pops just write twice the same unique FST value (e.g. 0.2 0.2)
• -model INT: 0=fixed errate 1=variable errate (uniform distribution) [1]
• -simpleRand INT: boolean [1]
• -seed INT: Random number seed [0]
• -base_freq FLOAT FLOAT FLOAT FLOAT: Background allele frequencies for A,C,G,T [0.25 0.25 0.25 0.25]
• -expansion INT: Very naive method to simulate population expansion, boolean [0]

Further examples can be found here.