Difference between revisions of "Arf"
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For arf 0.557215, we provide binaries for linux machines. | 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 | + | 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 arf. |
This page is maintained by [mailto:atks@umich.edu Adrian]. | This page is maintained by [mailto:atks@umich.edu Adrian]. |
Revision as of 17:00, 16 January 2012
arf is a genetic analysis program for sequencing data.
Basic Usage Example
arf [options] <vcf-file>
Here is an example of how arf
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: 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 arf.
This page is maintained by Adrian.