PSMC

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PSMC Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Module: Example

[]$ module spider psmc
---------------------
  psmc: psmc/1.0
---------------------
    This module can be loaded directly: module load psmc/1.0
    Help:
      Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model.
      see: https://github.com/lh3/psmc


[]$ module spider psmc/1.0
---------------------
  psmc: psmc/1.0
---------------------
    This module can be loaded directly: module load psmc/1.0
    Help:
      Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model.
      see: https://github.com/lh3/psmc
[]$ module load psmc/1.0

Using:

Remember to either:

  • Create an interactive session using salloc
  • Submit an sbatch job that calls srun.
  • Do NOT run directly on a login node.

Basic Command Line:

[]$ psmc
Program: psmc (Pairwise SMC Model)
Version: 0.6.5-r67
Contact: <http://hengli.uservoice.com/>

Usage:   psmc [options] input.txt

Options: -p STR      pattern of parameters [4+5*3+4]
         -t FLOAT    maximum 2N0 coalescent time [15]
         -N INT      maximum number of iterations [30]
         -r FLOAT    initial theta/rho ratio [4]
         -c FILE     CpG counts generated by cntcpg [null]
         -o FILE     output file [stdout]
         -i FILE     input parameter file [null]
         -T FLOAT    initial divergence time; -1 to disable [-1]
         -b          bootstrap (input be preprocessed with split_psmcfa)
         -S          simulate sequence
         -d          perform decoding
         -D          print full posterior probabilities


[]$ calD
Usage: calD [options] <U.fa> <V.fa> <X.fa> <Y.fa>
Options:
  -w INT     window size for block Jack-Knife [1000000]
  -q INT     quality threshold [0]
  -M FILE    mask regions in BED FILE [null]
  -s INT     step size (effective with -b) [100]
  -b         binary output

[]$ cntcpg
Usage: cntcpg [-b] [-s 100] [-n 0.9] <in.fa>
Output: 5 numbers: #CpG #CpG-ts #nonCpG #nonCpG-ts+tv #tv


[]$ fq2psmcfa
Usage: fq2psmcfa [-cnvx] [-q 10] [-g 10000] [-s 100] <in.fq>


[]$ mutDiff
Usage: mutDiff [-bl] [-s 100] <1.fa> <2.fa> <outgroup.fa>


[]$ splitfa
Usage: splitfa <in.fa> [trunk_size=500000]


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