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Here is an example of how <code>arf</code> works:
Here is an example of how <code>arf</code> works:
arf -s 1000g.vcf got2d.vcf -g hg18.fa -w 10 -d
#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
arf -s hwe 1000g.vcf
#estimates Inbreeding Coefficient F from genotype likelihood
arf -s f 1000g.vcf
# performs both HWE test and estimates F
arf -s hwe,f 1000g.vcf
# annotates exonic regions
arf -a exon 1000g.vcf
#computes a complexity measure for flanking sequences around a variant
arf -a c 1000g.vcf
== Command Line Options ==
== Command Line Options ==
