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#CPXY - complexity measure for flanks of length l defined by option -l, default is 25
#CPXY - complexity measure for flanks of length l defined by option -l, default is 25
arf -a complexity 1000g.vcf -g genome.fa -l 30
arf -a complexity 1000g.vcf -g genome.fa -l 30
== In development/Pending update ==
#annotates variants
##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
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 ==
== Download ==
== Download ==
For arf 0.557215, we provide binaries for linux machines [http://www-personal.umich.edu/~atks/arf arf].
For arf 0.557215, we provide binaries for linux machines [http://www-personal.umich.edu/~atks/arf arf 0.557215].
You will also need a copy of human genome assembly fasta file: [http://www-personal.umich.edu/~atks/human.g1k.v37.fa.gz human.g1k.v37.fa]. Please gunzip it before usage. arf will generate a memory mapped file from the fasta file named human.g1k.v37-bs.umfa.
You will also need a copy of human genome assembly fasta file: [http://www-personal.umich.edu/~atks/human.g1k.v37.fa.gz human.g1k.v37.fa]. Please gunzip it before usage. arf will generate a memory mapped file from the fasta file named human.g1k.v37-bs.umfa.
You will also need a copy of UCSC refGene text file: [http://www-personal.umich.edu/~atks/refGene.txt.gz refGene.txt.gz].
You will also need a copy of UCSC refGene text file: [http://www-personal.umich.edu/~atks/refGene.txt.gz refGene.txt].
This page is maintained by [mailto:atks@umich.edu Adrian].
This page is maintained by [mailto:atks@umich.edu Adrian].
