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57 bytes added
, 14:34, 27 January 2012
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| == In development == | | == In development == |
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− | #-c option directs the output to STDOUT | + | #annotates variants |
| + | ##INFO=<ID=,Number=1,Type=string,Description="Annotates variant by types SNP, MNP, INDEL, SV, CR"> |
| arf -a vartype 1000g.vcf | | arf -a vartype 1000g.vcf |
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− | #-o option specifies an output file name | + | #extracts GT fields from 1000g.vcf for the variants found in paltum.sit.vcf |
− | arf -a complexity 1000g.vcf -g genome.fa -l 30 -o paltum.vcf
| + | #-d specifies a data processing action |
− | | + | arf -d extract 1000g.chr1.vcf 1000g.ch2.vcf -f paltum.site.vcf |
− | #input VCF file can be gzipped | |
− | arf -a complexity 1000g.vcf.gz -g genome.fa -l 30 -o paltum.vcf | |
− | | |
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| == Command Line Options == | | == Command Line Options == |