View source for Arf

[[Category:Software]]
'''arf''' is a genetic analysis program for sequencing data.

== Basic Usage Example ==

  arf [options] <vcf-file>

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.
   #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 -a freq 1000g.vcf

   #conducts HWE LRT test from genotype likelihoods (multiallelic)
   #adds the info tags
   #HWP - HWE P-value
   #HWCHISQ - HWE Chi-square value
   #HWDOF - Degrees of freedom for test
   #will generate frequency tags.
   arf -a hwe 1000g.vcf

   #estimates Inbreeding coefficient F from genotype likelihood
   #adds the info tag
   #F - Inbreeding coefficient
   arf -a f 1000g.vcf

   #you can also do both analysis at the same time
   #performs both HWE test and estimates F
   arf -a hwe,f 1000g.vcf

   #annotates exonic regions
   #adds the info tag
   #EXON - flag  
   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
   #adds the info tag
   #FLANKS - 5' sequence, reference allele, 3' sequence up to length n defined by option -l, default is 25
   arf -a flanks 1000g.vcf -g genome.fa -l 30

   #computes a complexity measure for flanking sequences around a variant
   #adds the info tag
   #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

== Command Line Options ==

    vcf-file     VCF file (can be gzipped or bgzipped)
    g              genome-file (fasta file) 
                   (note that if genome.fa is specified, the actual file looked 
                    for is genome-bs.umfa, if the memory mapped file is not 
                    found, it will be automatically generated from the fasta file)
    l              length of flanking sequence (default is 25)
    a              analysis/annotation
    o              output file name  (default is arf.vcf)
    f              annotation file name (can be gzipped)

==  Output ==


    An output file is generated with the name arf.vcf
    The file name can be specified with the -o option.
    Log files are generated in arf.log

== Description ==

    Basically deals with VCF files, generate additional info tags in an output VCF file.

== Download ==

For arf 0.557215, we provide binaries for linux machines [http://www-personal.umich.edu/~atks/arf arf].
      
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]. 


This page is maintained by  [mailto:atks@umich.edu Adrian].