example of data set build using h3agwas pipeline and kgp project dataset

descriptif command line used

command line used to created dataset using h3agwas pipeline:

nextflow run h3abionet/h3agwas/utils/build_example_data/main.nf --pos_allgeno utils/h3agwas_all.pos  -resume -profile slurmSingularity --list_chro 1-22,X --list_chro_pheno 1-22 --output_dir allchro --output allchro

dataset, can be download here (mdm5 : 842ff36935cd8cc1784cb3db21b9c45f) has been build followed :

• extraction of h3abionet array positions
• position from array extracted from 1000Genome v37, release:20130502 and format in plink
• some sex has been changed to add error
• build a phenotype using gwas catalog
• 19 february 2021 from USCS
• Diabetes phenotype
• extraction of positions from gwas catalog of KGG
• Effect extracted of gwas catalog and simulation of phenotype using gcta ##descriptif folder ####utils : `
• h3agwas_all.pos` : contains list of position from h3abionet array

• allchro/geno_all
  *contains genotype in plink format from 2507 individuals of KGP and positions of h3abionet
• plink file : allchro.bed allchro.bim allchro.fam
• allchro_sexsex_change_plk.ind : list of individuals where sex has been changed to create sex error
• allchro/gwascat
• contains information relative to gwas catalog used to build dataset
• allchro/simul_pheno
• folder contains information relative to phenotype simulated :
• allchro/simul_pheno/datai/ : plink phenotype extracted from KGP corresponding at positions used to simulated phenotype
• allchro/simul_pheno/qual_pheno/allchro_ql.pheno : binary phenotype
• allchro/simul_pheno/quant_pheno/allchro_qt.pheno : quantitatif phenotype
• allchro/simul_pheno/pheno_format/ : information relative to positions to simulated phenotype

run h3agwas/qc on simulated data

nextflow -c utils/params_1000G_h3abionet.params run h3abionet/h3agwas/qc/main.nf -profile slurmSingularity -resume