Changes

   #HWDOF - Degrees of Freedom for test

   #HWDOF - Degrees of Freedom for test

   #will generate frequency tags.

   #will generate frequency tags.

   arf -s hwe 1000g.vcf

   arf -a hwe 1000g.vcf

   #conducts HWE LRT test from genotype likelihoods (multiallelic)

   #conducts HWE LRT test from genotype likelihoods (multiallelic)

   #will attempt to use existing allele frequency estimates in the info  

   #will attempt to use existing allele frequency estimates in the info  

   arf -s hwe 1000g.vcf -e

   arf -a hwe 1000g.vcf -e

   #estimates Inbreeding Coefficient F from genotype likelihood

   #estimates Inbreeding Coefficient F from genotype likelihood

   #adds the info tag

   #adds the info tag

   #F - Inbreeding Coefficient

   #F - Inbreeding Coefficient

   arf -s f 1000g.vcf

   arf -a f 1000g.vcf

   #you can also do both analysis at the same time

   #you can also do both analysis at the same time

   #performs both HWE test and estimates F

   #performs both HWE test and estimates F

   arf -s hwe,f 1000g.vcf

   arf -a hwe,f 1000g.vcf

      

      

   #annotates exonic regions

   #annotates exonic regions