SimLinkedBSFS

Description

SimLinkedBSFS is a C++ wrapper for the popular command line software for simulating population genetic samples ms. The role of SimLinkedBSFS is to generate a bSFS (or blockwise Site Frequency Spectrum) from the ms output which is already in blocks but in a sequence format. SimLinkedBSFS is most useful when simulating large stretches of sequence (say 1Mbp in size) but when the bSFS needs to be generated from much smaller blocks (say 2Kb in size).

Install instructions

It is easiest to build a SimLinkedBSFS binary under all flavours of Linux. SimLinkedBSFS requires the GNU Compiler Collection (gcc). If you do not have gcc, you can use your OS specific package handling utility (under Debian/Ubuntu) :

sudo apt-get install build-essential

1. Once gcc is available, run

   wget https://github.com/champost/SimLinkedBSFS/archive/master.tar.gz
   

2. Untar the archive using

   tar -xzf master.tar.gz
   

3. Change directory

    cd SimLinkedBSFS-master
   

4. Make the compile script executable

    chmod +x compile.sh
   

5. Compile SimLinkedBSFS

    ./compile.sh
   

If you want SimLinkedBSFS to be accessible from anywhere, such as your data folder, you might want to

cp SimLinkedBSFS ~/bin

This ensures that you can execute the program by specifying SimLinkedBSFS ... instead of ./SimLinkedBSFS ... from the installation folder. This holds only if ~/bin exists and is part of your $PATH environment variable.

Usage

The commands for SimLinkedBSFS are almost entirely in the ms format. For example we would like to simulate a 2 population scenario consisting of 5 and 2 haploid samples respectively. The command below will simulate 100000 sequences of length 4000 bp.

ms 7 100000 -t 1 -r 0.5 4001 -I 2 5 2 -m 1 2 1 -ej 1.25 1 2

Now let us assume that we want to create a bSFS consisting of 1000 bp blocks. We start by creating a file named popconfig.txt containing the number of samples per population. Here it would be :

echo 5 2 > popconfig.txt

Next, we can run SimLinkedBSFS as follows :

SimLinkedBSFS 7 100000 -t 1 -r 0.5 4001 -I 2 5 2 -m 1 2 1 -ej 1.25 1 2 A B C D > my_two_pop_bSFS.txt

Here A, B, C, D are what differentiate it from the ms command line.

A : a value z (0 < z <= 1) giving the block size (here it would be 4000 X z = 1000, so z = 0.25)
B : number of mutations per branch class or Kmax (please refer to the bSFS literature). 0 means no Kmax.
C : number of simulated populations (here it will be 2)
D : a lowercase "f" or "u", saying you want the folded or unfolded bSFS respectively

Finally, the command line for generating a folded bSFS from 1000 bp blocks and no Kmax would be :

SimLinkedBSFS 7 100000 -t 1 -r 0.5 4001 -I 2 5 2 -m 1 2 1 -ej 1.25 1 2 0.25 0 2 f > my_two_pop_bSFS.txt