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, 11:40, 18 January 2012
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| #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 |