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Arf (view source)

Revision as of 18:38, 17 January 2012

202 bytes removed ,  18:38, 17 January 2012
→‎Basic Usage Example
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   #conducts HWE LRT test from genotype likelihoods (multiallelic)
 
   #conducts HWE LRT test from genotype likelihoods (multiallelic)
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  #adds the info tags
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  #HWP - HWE P-value
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  #HWCHISQ - HWE Chisquare value
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  #HWDOF - Degrees of Freedom for test
   
   #will attempt to use existing allele frequency estimates in the info  
 
   #will attempt to use existing allele frequency estimates in the info  
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  #fields if they exist, otherwise it will estimate the frequencies from the data.
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    arf -s hwe 1000g.vcf -e
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  arf -s hwe 1000g.vcf -e
      
   #estimates Inbreeding Coefficient F from genotype likelihood
 
   #estimates Inbreeding Coefficient F from genotype likelihood
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