Annotation Exercise

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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 id dbNSFP.GERP_RS dbNSFP.phyloP100way_vertebrate dbNSFP.phastCons100way_vertebrate
vtools select 5var --output chr pos ref alt dbNSFP.FATHMM_pred dbNSFP.FATHMM_score
vtools select 5var --output chr pos ref alt dbNSFP.Polyphen2_HDIV_pred dbNSFP.Polyphen2_HDIV_score dbNSFP.Polyphen2_HVAR_pred dbNSFP.Polyphen2_HVAR_score
vtools select 5var --output chr pos ref alt dbNSFP.LRT_pred dbNSFP.LRT_score
vtools select 5var --output chr pos ref alt dbNSFP.MutationTaster_pred
vtools select 5var --output chr pos ref alt dbNSFP.PROVEAN_pred dbNSFP.PROVEAN_score
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