Annotation Exercise
From Statistical Genetics Courses
Revision as of 18:48, 23 February 2017 by Serveradmin (Talk | contribs) (Created page with "__NOTITLE__ ==Annotation exercise== vtools init APOC3 vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19 vtools select variant --count vtools use refG...")
Annotation exercise
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
