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#annotates variants
#annotates variants
##INFO=<ID=,Number=1,Type=string,Description="Annotates variant by types SNP, MNP, INDEL, SV, CR">
##INFO=<ID=,Number=1,Type=string,Description="Annotates variant by types SNP, MNP, INDEL, SV, CR">
arf -a vartype 1000g.vcf
#-l option defines the length in which to differentiate INDELs and SVs
arf -a vartype 1000g.vcf -l 30
#extracts GT fields from 1000g.vcf for the variants found in paltum.sit.vcf
#extracts GT fields from 1000g.vcf for the variants found in paltum.sit.vcf
