james-guevara / pydnm

Python clone of ForestDNM

pyDNM

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Classifier used to discover single-nucleotide variant (SNV) de novo mutations (DNMs) and indel DNMs.

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⚠️ Still under construction 🚧 USE AT YOUR OWN RISK

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Install

$ pip install https://github.com/dantaki/pydnm/releases/download/v0.1.0.0/pyDNM-0.1.0.0.tar.gz 

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Usage

usage: 
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 888    888 888   888    888    888  88 888o88    88 888o8 88  
 888    888  888 888     888    888  88   8888    88  888  88  
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Python port of forestDNM for SNVs+INDELs : http://sebatlab.ucsd.edu/software-data 
Version 0.1.0.0    Authors: Danny Antaki, Aojie Lian, James Guevara    
                   Contact: dantaki at ucsd dot edu
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    pyDNM  -f <in.fam>  -v  <in.vcf>  [-oLgkVh]
    
input arguments:
  
  -v, -vcf    PATH    vcf file
  -f, -fam    PATH    plink fam file
  
optional arguments:

  -o, -out    PATH    output file
  -L, -log    PATH    log file for standard error messages [default: STDOUT]
  -g  -gen    STR     human reference genome version [default: hg38]
  -k                  keep false positive de novos in output
  -V                  print extra warnings
  
  -h, -help           show this message and exit