==Annotation exercise==
mkdir APOC3 && cd APOC3
vtools init APOC3
vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19
vtools select variant --count
vtools use refGene
vtools show fields
vtools select variant --output chr pos ref alt refGene.name2
vtools use ../data/dbNSFP.DB
vtools show fields
vtools select variant 'id="rs76353203" or id="rs140621530" or id="rs147210663" or id="rs121918381" or id="rs121918382"' -t 5var
vtools select 5var --output chr pos ref alt dbNSFP.SIFT_pred dbNSFP.SIFT_score
vtools select 5var --output chr pos ref alt dbNSFP.CADD_raw dbNSFP.CADD_phred
==GATK/IGV exercise==