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Arf (view source)

Revision as of 16:54, 17 January 2012

363 bytes added ,  16:54, 17 January 2012
→‎Basic Usage Example
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   #HWCHISQ - HWE Chisquare value
 
   #HWCHISQ - HWE Chisquare value
 
   #HWDOF - Degrees of Freedom for test
 
   #HWDOF - Degrees of Freedom for test
 +
  #AF - Allele frequency estimates of alternate alleles (EM)
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  #HWEAF - Allele frequency estimates of alternate alleles under the assumption of HWE equilibrium (EM)
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  #GF - Genotype frequency estimates (EM)
 
   arf -s hwe 1000g.vcf  
 
   arf -s hwe 1000g.vcf  
    
   #estimates Inbreeding Coefficient F from genotype likelihood
 
   #estimates Inbreeding Coefficient F from genotype likelihood
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  #adds the info tag
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  #F - Inbreeding Coefficient
 
   arf -s f 1000g.vcf
 
   arf -s f 1000g.vcf
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   # annotates exonic regions
 
   # annotates exonic regions
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  #adds the info tag
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  #EXON - flag
 
   arf -a exon 1000g.vcf
 
   arf -a exon 1000g.vcf
    
   #computes a complexity measure for flanking sequences around a variant
 
   #computes a complexity measure for flanking sequences around a variant
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   arf -a c 1000g.vcf
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  #adds the info tag
 +
  #C - complexity measure
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   arf -a c 1000g.vcf -g genome.fa
    
== Command Line Options ==
 
== Command Line Options ==
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