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, 16:59, 16 January 2012
[[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:
arf -s 1000g.vcf got2d.vcf -g hg18.fa -w 10 -d
== Command Line Options ==
vcf-file VCF file (can be gzipped or bgzipped)
g genome-file (Memory Mapped Sequence file)
(note that if genome.fa is specified, the actual file looked for is genome-bs.umfa)
s statistical analysis
a annotation
== Output ==
user@host:~$ vmatch gatk.vcf samtools.vcf -w 10 -d
== Description ==
Outputs 2 files
match.txt : gives the matched pairs
1)id1
2)id2
3)match type
4)extended no of bases
5)normalized
match.log : Details of the extension and normalization process for all compared pairs
vmatch matches the variants in 2 VCF files by choosing the best match for every
possible variant pair. The percentage of matches is given at 3 levels for each
variant total of both VCF files.
== Download ==
For arf 0.557215, we provide binaries for linux machines.
You will also need a copy of the memory mapped file: [http://www-personal.umich.edu/~atks/human.g1k.v37-bs.umfa.gz human.g1k.v37-bs.umfa]. Please gunzip it before usage. Note that to use it, please refer to the file as human.g1k.v37.fa, it will be automatically renamed as human.g1k.v37-bs.umfa by vmatch.
This page is maintained by [mailto:atks@umich.edu Adrian].