Difference between revisions of "Annotation Exercise"
From Statistical Genetics Courses
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Serveradmin (Talk | contribs) (→Annotation exercise) |
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==Annotation exercise== | ==Annotation exercise== | ||
| − | + | mkdir APOC3 | |
| + | cd APOC3 | ||
vtools init APOC3 | vtools init APOC3 | ||
vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19 | vtools import ../data/APOC3.vcf --format ../data/vcf.fmt --build hg19 | ||
Latest revision as of 16:55, 2 March 2017
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
