Individuals Level Filtering sexcheck

Framingham
Process 5
the binary file that contains the
NP1: step4
Data Import Check discordant sex raw genotype data
ped map txt
plink
Framingham Framingham fail-sex-qc
Process 6
—bfile Framingham NP1: step5
Genotype file SNP map file Individual with sex discrepancy
—check-sex Select Sex Problem Individual

—out Framingham Bash Shell

Process 9
Process 3
to calculate the mean homozygosity rate NP1: step9
NP1: step 3
Make BED file bed across X-chromosome markers for each Plot Heter vs. Missing txt
Framingham individual in the study fail-qc-inds
plink miss-vs-het.Rscript Process 13
the binary file that contains the NP1: step20 Failed individual; to be removed
—file raw-GWA-data Concentrate all failed individual
raw genotype data from consideration
log —make-bed Bash Shell
Framingham Process 7
—out raw-GWA-data
NP1: step7 Genotype and heterozygosity rate
Running log Process 14
imiss
plink NP1: step21
Framingham Removal of failed individual
—bfile Framingham
fam Missing genotype rate for plink
Framingham —missing (i)ndividual
Framingham.imiss-vs-het.pdf txt —file raw-GWA-data
.fam which is just the first six bim —out Framingham fail-imisshet-qc
—remove fail-qc-inds.txt
columns of .ped. Framingham lmiss
to calculate the missing data rates Failed individual; to be removed
Framingham —make-bed
a revsied map file .bim which from consideration
contains two extra columns that Missing genotype rate for SNP —out clean-inds-GWA-data
give the allele names for each
SNP Process 8
NP1: step8
Calculate heterozygosity rate
plink
het Process 10
—bfile Framingham Framingham NP1: step10
—het Heterozygosity rate Select genotype and heterozygosity
problems
—out Framingham
miss-vs-het-cutoff.Rscript
to calculate the outlying heterozygosity
rate

Process 16
NP1: step23 Plot histogram & Extract
failed marker txt
clean-ind-Hist.Rscript fail-lmiss-qc
imiss txt
SNP with excessing
clean-inds-Framingham fail-markers-qc
Process 15 missing data
bed NP1: step22 Missing genotype rate for markers with
Process 21
clean-inds-Framingham Calculate marker missing genotype (i)ndividual excessing missing
NP1: step25.1 data
Finalize marker filter
the binary file that contains the plink Process 17
Concentrate all failed marker
raw genotype data NP1: step23.2
—bfile clean-inds-Framingham
lmiss Extract Failed marker Bash Shell
—missing clean-inds-Framingham
Bash Shell
Process 22
—out clean-inds-Framingham Missing genotype rate for SNP
NP1: step26
Column QC Finalize
Process 19 Removal of failed marker
NP1: step25 plink
Process 18 Extract P < 0.0001
NP1: step24 txt
Calculate genotype call missing —file raw-GWA-data
Bash Shell fail-diffmiss-qc
rates between cases and control clean-inds-Framingham
—exclude fail-markers-qc.txt
Missing data rate
plink Call rates
between cases and —maf 0.01
—bfile clean-inds-Framingham controls
—geno 0.05
—test-missing —hwe 0.00001
—out clean-inds-Framingham —make-bed
—out clean-GWA-data
Marker Level Filtering

Statistical Analysis Process 23A1

NP2: step2 Result Interpretation
chi-square with PED default
assoc
plink
Framingham-result
—bfile clean-Framingham
Associate analysis results Process 25
—assoc NP1: step10
Result Annotation
—out Framingham-result
Result_Interpretation.Rscript

Process 23A2 assoc

NP2: step2 Framingham-adjusted-result
chi-square with PED default:
Multiple Comparison Correction Adjustment Associate analysis results
plink
—bfile clean-Framingham
bed assoc
clean-Framingham —assoc
covar-SEX
the binary file that contains the —out Framingham-result
Associate analysis results
genotype data
Process 24
Process 23B1 NP1: step10
NP2: step2.1
Plot Mahattan and QQ plots Data Visualization
chi-square with co-var file: SEX manhattan-plot.Rscript
plink
—bfile clean-Framingham assoc
covar-ASTHMA
—pheno Framingham-Asthma.cov
Associate analysis results
-- pheno-name SEX
-- out covar-SEX
-- assoc

Process 23B2
NP2: step2.1
chi-square with co-var file: ASTHMA
plink
model
—bfile clean-Framingham
Framingham-model
—pheno Framingham-Asthma.cov
Associate analysis results
-- pheno-name ASTHMA
-- out covar-ASTHMA
-- assoc

Process 23C
NP2: step4(A)
chi-square testing all model
plink
—bfile clean-Framingham
-- model
-- out Framingham-model