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