Difference between revisions of "PSEQ Commands in Exercise"

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__NOTITLE__
 
__NOTITLE__
  
==Regression exercise==
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==PSEQ Commands in Exercise==
In R:
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<pre>pseq help
 
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pseq help all
load("dbp.R")
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pseq myproj new-project --resources hg19
ls()
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pseq myproj load-vcf --vcf CEU.exon.2010_03.genotypes.hg19.vcf.gz YRI.exon.2010_03.genotypes.hg19.vcf.gz
dbp[1:5,]
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pseq myproj load-pheno --file phenotype.phe
#
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pseq myproj v-view | head
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pseq myproj i-view | head
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pseq myproj summary
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pseq myproj var-summary
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pseq myproj ind-summary
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pseq myproj loc-summary
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pseq myproj ref-summary
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pseq myproj seq-summary
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pseq myproj file-summary
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pseq myproj meta-summary
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pseq myproj v-stats
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pseq myproj i-stats | head
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pseq myproj tag-file --id 1 --name CEU
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pseq myproj tag-file --id 2 --name YRI
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pseq myproj var-summary
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pseq myproj v-freq | head
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pseq myproj v-freq --mask file=CEU | head
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pseq myproj v-freq --mask file=YRI | head
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pseq myproj v-view --mask any.filter.ex | head
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pseq myproj v-view --mask any.filter.ex | wc -l
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pseq myproj v-view --mask any.filter | wc -l
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pseq myproj var-set --group pass --mask any.filter.ex
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pseq myproj var-summary
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pseq myproj var-set --group pass_DP15 --mask include="DP>14" var=pass
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pseq myproj var-summary
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pseq myproj var-set --group pass_DP15_DPgeno10 --mask geno=DP:ge:11 var=pass_DP15
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pseq myproj var-summary
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pseq myproj var-set --group pass_DP15_DPgeno10_CEU --mask file=CEU var=pass_DP15_DPgeno10
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pseq myproj var-summary
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pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE --mask hwe=5.7e-7:1 var=pass_DP15_DPgeno10_CEU
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pseq myproj var-summary
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pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE_MAFgt05 --mask maf=0.05:0.5 var=pass_DP15_DPgeno10_CEU_HWE
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pseq myproj var-summary
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pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE_MAFlt01 --mask "mac=1 maf=0.01" var=pass_DP15_DPgeno10_CEU_HWE
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pseq myproj var-summary
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pseq myproj glm --phenotype BMI --covar SEX --mask var=pass_DP15_DPgeno10_CEU_HWE_MAFgt05 > SNV_CEU.result
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head SNV_CEU.result
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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
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pseq myproj assoc --tests fw vt --phenotype BMI
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pseq myproj assoc --tests skat --phenotype BMI --covar SEX --mask var=pass_DP15_DPgeno10_CEU_HWE_MAFlt01 loc.group=refseq > SKAT_CEU.result
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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
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head -20 SKAT_CEU.result
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cat SKAT_CEU.result | grep SKAT | grep -v "P=NA" | sort -k6 | head -15
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</pre>

Latest revision as of 15:56, 6 June 2018

PSEQ Commands in Exercise

pseq help
pseq help all
pseq myproj new-project --resources hg19
pseq myproj load-vcf --vcf CEU.exon.2010_03.genotypes.hg19.vcf.gz YRI.exon.2010_03.genotypes.hg19.vcf.gz
pseq myproj load-pheno --file phenotype.phe
pseq myproj v-view | head
pseq myproj i-view | head
pseq myproj summary 
pseq myproj var-summary
pseq myproj ind-summary
pseq myproj loc-summary
pseq myproj ref-summary
pseq myproj seq-summary
pseq myproj file-summary
pseq myproj meta-summary
pseq myproj v-stats
pseq myproj i-stats | head
pseq myproj tag-file --id 1 --name CEU
pseq myproj tag-file --id 2 --name YRI
pseq myproj var-summary
pseq myproj v-freq | head 
pseq myproj v-freq --mask file=CEU | head
pseq myproj v-freq --mask file=YRI | head
pseq myproj v-view --mask any.filter.ex | head
pseq myproj v-view --mask any.filter.ex | wc -l
pseq myproj v-view --mask any.filter | wc -l
pseq myproj var-set --group pass --mask any.filter.ex
pseq myproj var-summary
pseq myproj var-set --group pass_DP15 --mask include="DP>14" var=pass
pseq myproj var-summary
pseq myproj var-set --group pass_DP15_DPgeno10 --mask geno=DP:ge:11 var=pass_DP15
pseq myproj var-summary
pseq myproj var-set --group pass_DP15_DPgeno10_CEU --mask file=CEU var=pass_DP15_DPgeno10
pseq myproj var-summary
pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE --mask hwe=5.7e-7:1 var=pass_DP15_DPgeno10_CEU
pseq myproj var-summary
pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE_MAFgt05 --mask maf=0.05:0.5 var=pass_DP15_DPgeno10_CEU_HWE
pseq myproj var-summary
pseq myproj var-set --group pass_DP15_DPgeno10_CEU_HWE_MAFlt01 --mask "mac=1 maf=0.01" var=pass_DP15_DPgeno10_CEU_HWE
pseq myproj var-summary
pseq myproj glm --phenotype BMI --covar SEX --mask var=pass_DP15_DPgeno10_CEU_HWE_MAFgt05 > SNV_CEU.result 
head SNV_CEU.result
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
pseq myproj assoc --tests fw vt --phenotype BMI 
pseq myproj assoc --tests skat --phenotype BMI --covar SEX --mask var=pass_DP15_DPgeno10_CEU_HWE_MAFlt01 loc.group=refseq > SKAT_CEU.result
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
head -20 SKAT_CEU.result
cat SKAT_CEU.result | grep SKAT | grep -v "P=NA" | sort -k6 | head -15