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== In development ==
== In development ==
#-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
#-o option specifies an output file name
#extracts GT fields from 1000g.vcf for the variants found in paltum.sit.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
== Command Line Options ==
== Command Line Options ==
