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Here is an example of how <code>arf</code> works:
Here is an example of how <code>arf</code> works:
#estimates allele and genotype frequencies from genotype likelihoods.
#AF - Allele frequency estimates of alternate alleles (EM)
#HWEAF - Allele frequency estimates of alternate alleles under the assumption of HWE equilibrium (EM)
#GF - Genotype frequency estimates (EM)
arf -s freq 1000g.vcf
#conducts HWE LRT test from genotype likelihoods (multiallelic)
#conducts HWE LRT test from genotype likelihoods (multiallelic)
#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)
#will generate frequency tags.
#HWEAF - Allele frequency estimates of alternate alleles under the assumption of HWE equilibrium (EM)
arf -s hwe 1000g.vcf
#GF - Genotype frequency estimates (EM)
arf -s hwe 1000g.vcf
#conducts HWE LRT test from genotype likelihoods (multiallelic)
#adds the info tags
#HWP - HWE P-value
#HWCHISQ - HWE Chisquare value
#HWDOF - Degrees of Freedom for test
#will attempt to use existing allele frequency estimates in the info
#fields if they exist, otherwise it will estimate the frequencies from the data.
arf -s hwe 1000g.vcf -e
#estimates Inbreeding Coefficient F from genotype likelihood
#estimates Inbreeding Coefficient F from genotype likelihood
arf -s f 1000g.vcf
arf -s f 1000g.vcf
# performs both HWE test and estimates F
#you can also do both analysis at the same time
#performs both HWE test and estimates F
arf -s hwe,f 1000g.vcf
arf -s hwe,f 1000g.vcf
# annotates exonic regions
#annotates exonic regions
#adds the info tag
#adds the info tag
#EXON - flag
#EXON - flag
