The streaming service that annotates vcf records with background allele frequencies found in 1000G and ExAC projects
This utility requires a database file pre-filled with allele frequencies in 1000G and ExAC to work properly. The file need to be at afdata/af.db relative to the current directory. The utility 'vcfload' can be used to generate this file
afbgalive [-z]
vcf records are read directly from stdin. If '-z' is specified, the output is then in bgzip compressed from
This utility is used to read allele frequency information from 1000G or ExAC vcf files, and populate a sqlite database
vcfload <db_filename> <tablename> < file
db_filename is the database file that will be eventually provided to afbgalive.
tablename can either be 'g1k' or 'exac', depending on which vcf file is provided as input
file is the published vcf file from 1000G or ExAC project
After importing all vcf files, a composite (chrom,pos) index needs to be created on both g1k and exac table manually to achieve reasonable performance.