pyfreq

cython optimized allele frequency calculation for VCFs

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install

$ pip install pyfreq

usage

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pyfreq: compute allele frequency for VCF files
Version 0.0.1    Author: Danny Antaki <dantaki at ucsd dot edu>    github.com/dantaki/pyfreq

  pyfreq   -v <in.vcf>   -f <in.fam> [-LoPh]

input arguments: 
 
  -v, -vcf       PATH     vcf file  
  -f, -fam       PATH     plink fam file
 
optional arguments:
  
  -L, -log       PATH    log file for standard error messages [default: STDOUT]
  -o, -out       PATH    output prefix [default: pyfreq.out]
  -P, -prog              display a progress bar

  -h, -help              show this message and exit