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2015-march-berlin-commands

77 bytes removed, 17:17, 7 June 2016
/* PLINKSEQ exercise */
Data analysis:
pseq help<br data-attributes="%20/" />pseq help all<br data-attributes="%20/" />pseq myproj new-project --resources hg19<br data-attributes="%20/" />pseq myproj load-vcf --vcf CEU.exon.2010_03.genotypes.hg19.vcf.gz YRI.exon.2010_03.genotypes.hg19.vcf.gz<br data-attributes="%20/" />pseq myproj load-pheno --file phenotype.phe<br data-attributes="%20/" />pseq myproj v-view | head<br data-attributes="%20/" />pseq myproj i-view | head<br data-attributes="%20/" />pseq myproj summary <br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj ind-summary<br data-attributes="%20/" />pseq myproj loc-summary<br data-attributes="%20/" />pseq myproj ref-summary<br data-attributes="%20/" />pseq myproj seq-summary<br data-attributes="%20/" />pseq myproj file-summary<br data-attributes="%20/" />pseq myproj meta-summary<br data-attributes="%20/" />pseq myproj v-stats<br data-attributes="%20/" />pseq myproj i-stats | head<br data-attributes="%20/" />pseq myproj tag-file --id 1 --name CEU<br data-attributes="%20/" />pseq myproj tag-file --id 2 --name YRI<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj v-freq | head<br data-attributes="%20/" />pseq myproj v-freq --mask file=CEU | head <br data-attributes="%20/" />pseq myproj v-freq --mask file=YRI | head<br data-attributes="%20/" />pseq myproj v-view --mask any.filter.ex | head<br data-attributes="%20/" />pseq myproj v-view --mask any.filter.ex | wc -l<br data-attributes="%20/" />pseq myproj v-view --mask any.filter | wc -l<br data-attributes="%20/" />pseq myproj var-set --group pass --mask any.filter.ex<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj var-set --group pass_DP15 --mask include="DP>14" var=pass<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj var-set --group pass_DP15_DPgeno10 --mask geno=DP:ge:11 var=pass_DP15<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj var-set --group pass_DP15_DPgeno10_CEU --mask file=CEU var=pass_DP15_DPgeno10<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE --mask hwe=5.7e-7:1 var=pass_DP15_DPgeno10_CEU<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE_MAFgt05 --mask maf=0.05:0.5 var=pass_DP15_DPgeno10_CEU_HWE<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE_MAFlt01 --mask "mac=1 maf=0.01" var=pass_DP15_DPgeno10_CEU_HWE<br data-attributes="%20/" />pseq myproj var-summary<br data-attributes="%20/" />pseq myproj glm --phenotype BMI --covar SEX --mask var=pass_DP15_DPgeno10_CEU_HWE_MAFgt05 > SNV_CEU.result <br data-attributes="%20/" />head SNV_CEU.result<br data-attributes="%20/" />cat SNV_CEU.result | awk '{if(FNR==1) print $0; if(NR>1) print $0 | "sort -k9"}' | grep -v "NA\s\+NA\s\+NA" | head<br data-attributes="%20/" />pseq myproj assoc --tests fw vt --phenotype BMI <br data-attributes="%20/" />pseq myproj assoc --tests skat --phenotype BMI --covar SEX --mask var=pass_DP15_DPgeno10_CEU_HWE_MAFlt01 loc.group=refseq > SKAT_CEU.result<br data-attributes="%20/" />pseq myproj assoc --tests skat --phenotype BMI --covar SEX --mask include="DP>14" geno=DP:ge:11 file=CEU hwe=5.7e-7:1 "mac=1 maf=0.01" loc.group=refseq > SKAT_CEU.result<br data-attributes="%20/" />head -20 SKAT_CEU.result<br data-attributes="%20/" />cat SKAT_CEU.result | grep SKAT | grep -v "P=NA" | sort -k6 | head -15
Exercise&nbsp;analyzing YRI samples: