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Here is an example of how <code>arf</code> works:
Here is an example of how <code>arf</code> works:
#-c option directs the output to STDOUT
arf -a complexity 1000g.vcf -g genome.fa -l 30 -c
#-o option specifies an output file name
arf -a complexity 1000g.vcf -g genome.fa -l 30 -o paltum.vcf
#input VCF file can be gzipped
arf -a complexity 1000g.vcf.gz -g genome.fa -l 30 -o paltum.vcf
#estimates allele and genotype frequencies from genotype likelihoods.
#estimates allele and genotype frequencies from genotype likelihoods.
#EXON - flag
#EXON - flag
arf -a exons 1000g.vcf -f refGene.txt
arf -a exons 1000g.vcf -f refGene.txt
#reference file can be gzipped up
arf -a exons 1000g.vcf -f refGene.txt.gz
#computes extracts flanking sequence around a variant
#computes extracts flanking sequence around a variant
