Scripts for body composition GWAS in UK Biobank
- Folder structure
- Phenotype
- Extract columns from UKBB files (awk)
- Exclusion [phenotype_an_free.R]
- Descriptives
- Covariates
- Regression [regression_linear.R]
- Transfer descriptives into doc
- Make scatterplots [plotting_descriptives_healthy.R]
- Make phenotypic correlation matrix
- Calculate independent tests
- Make correlation heatmap [full_correlation_alphabetical_healthy.R]
- GWAS
- per chromosome [gwas_chr.sh]
- Post-GWAS filtering [post_gwas_filtering/]
- Remove SNP duplicates [concatenate_filtering.sh]
- Retain HRC SNPs
- Cocatenate to one sumstats file
- Post-GWAS filtering 2 [post_gwas_filtering]
- MAF 0.01 [maf_0.01.sh]
- Meta-analyse
- Metal [bfpc_h_metal_se.script & metal_jobscript_bfpc.sh]
- Make sex-specific and metal files [sex_specific_sumstats_files/]
- [sex_sumstats.sh]
- [metal_sumstats.sh]
- [add_pos_to_meta_sumstats.sh]
- Extract gws SNPs [post_gwas_filtering/]
- Genome-wide significant SNPs [sign_snps.sh]
- gzip
- Put in spreadsheet
- Plots [plots]
- qqplot
- sex-specific qqplot
- Manhattan plot
- Miami plot
- Clumping
- FUMA
- Annotate
- FUMA
- LDSC [ldsc]
- Munge
- Calculate h2
- Put inflation statistics into table
- run rgs
- Part heritability [ldsc_part_h2]
- submit script