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arf -a complexity 1000g.vcf -g genome.fa -l 30
arf -a complexity 1000g.vcf -g genome.fa -l 30
== In development ==
== In development/Pending update ==
#annotates variants
#annotates variants
##INFO=<ID=,Number=1,Type=string,Description="Annotates variant by types SNP, MNP, INDEL, SV, CR">
##INFO=<ID=VTYPE,Number=1,Type=string,Description="Annotates variant by types SNP, MNP, INDEL, SV, CR">
#-l option defines the length in which to differentiate INDELs and SVs
#-l option defines the length in which to differentiate INDELs and SVs
arf -a vartype 1000g.vcf -l 30
arf -a vartype 1000g.vcf -l 30
#compute [[Genotype Likelihood Based Allele Balance]]
##INFO=<ID=AB,Number=1,Type=float,Description="Allele Balance computed from genotype likelihoods">
#requires PL/GL and DP in the genotype fields
arf -a ab 1000g.vcf
#-e option
#when used in conjunction with an analysis that requires allele or genotype frequency estimates,
#will attempt to find estimates in the AF, GF and HWEAF fields
arf -a ab 1000g.vcf -e
== Command Line Options ==
== Command Line Options ==
