Difference between revisions of "PSEQ Commands in Exercise"
From Statistical Genetics Courses
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==Regression exercise== | ==Regression exercise== | ||
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| + | <pre> | ||
pseq help | pseq help | ||
pseq help all | pseq help all | ||
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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 | 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 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 | ||
| + | </pre> | ||
Revision as of 15:54, 6 June 2018
Regression 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
