Skip to content

MSMC

MSMC (The multiple sequentially Markovian coalescent) is a method to infer population size and gene flow from multiple genome sequences.

MSMC is available as a module on Apocrita.

Usage

To run the latest installed version of MSMC, simply load the msmc module:

module load msmc

For usage documentation, run msmc -h.

Example job

MSMC can take several input files, one for each chromosome. These files contain a segregating site, including a column to denote how many sites have been called since the last segregating site.

An example input file:

1    58432     63      TCCC
1    58448     16      GAAA
1    68306     15      CTTT
1    68316     10      TCCC
1    69552     8       GCCC
1    69569     17      TCCC
1    801848    9730    CCCA
1    809876    1430    AAAG
1    825207    1971    CCCT,CCTC
1    833223    923     TCCC

Serial job

Here is an example job running on 2 cores and 2GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load msmc

msmc --fixedRecombination \
     --outFilePrefix out \
     --nrThreads ${NSLOTS} \
     example.txt

References