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arf [options] <vcf-file>
arf [options] <vcf-file>
Here is an example of how <code>arf</code> works:
Here are examples 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
#multiple analyses/annotations at once is possible
arf -a complexity,f,hwe,exons 1000g.vcf.gz -g genome.fa -l 30 -o paltum.vcf -f refGene.txt.gz
#estimates allele and genotype frequencies from genotype likelihoods.
#estimates allele and genotype frequencies from genotype likelihoods.
#adds the info tag
#adds the info tag
#EXON - flag
#EXON - flag
arf -a exon 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
#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 ==
vcf-file VCF file (can be gzipped or bgzipped)
vcf-file VCF file (can be gzipped or bgzipped)
h help page
g genome-file (fasta file)
g genome-file (fasta file)
(note that if genome.fa is specified, the actual file looked
(note that if genome.fa is specified, the actual file looked
for is genome-bs.umfa, if the memory mapped file is not
for is genome-bs.umfa, if the memory mapped file is not
found, it will be automatically generated from the fasta file)
found, it will be automatically generated from the fasta file)
l length of flanking sequence
l length of flanking sequence (default is 25)
a analysis/annotation
a analysis/annotation
o output file name
o output file name (default is arf.vcf)
f annotation file name (can be gzipped)
f annotation file name (can be gzipped)
== Download ==
== Download ==
For arf 0.557215, we provide binaries for linux machines.
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 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].
