Changes

   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 ==

   #-c option directs the output to STDOUT

   arf -a vartype 1000g.vcf

   #-l option defines the length in which to differentiate INDELs and SVs

   arf -a vartype 1000g.vcf -l 30

   #-o option specifies an output file name

   #compute [[Genotype Likelihood Based Allele Balance]]

   arf -a complexity 1000g.vcf -g genome.fa -l 30 -o paltum.vcf

   ##INFO=<ID=AB,Number=1,Type=float,Description="Allele Balance computed from genotype likelihoods">

 

   #requires PL/GL and DP in the genotype fields

   #input VCF file can be gzipped

   arf -a ab 1000g.vcf

   arf -a complexity 1000g.vcf.gz -g genome.fa -l 30 -o paltum.vcf

== 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].