Using the GTEx V8 data, I performed GCTA analysis. The genotype file exists in
/gpfs/data/im-lab/nas40t2/Data/GTEx/V8/genotype/plink_files/GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.SHAPEIT2_phased.vcf.gz
From there, I converted the vcf file into plink format using
plink2 --vcf /gpfs/data/im-lab/nas40t2/Data/GTEx/V8/genotype/GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.SHAPEIT2_phased.vcf.gz --make-bed --double-id --out /gpfs/data/im-lab/nas40t2/Data/GTEx/V8/genotype/plink_files/GTEX_ new
Note: without the --double-id plink will create the .fam file with FID being zero
I then created a grm using the plink files
gcta --bfile /gpfs/data/im-lab/nas40t2/Data/GTEx/V8/genotype/plink_files/GTEX_new /--autosome --maf 0.01 --make-grm --out /gpfs/data/im-lab/nas40t2/Data/GTEx/V8/genotype/plink_files/GTEX_grm_output
I then edited the phenotype file (gtex_cortex_models_10_10_20.xlsx) to the gcta format Check analysis for code to create phenotype file
I then ran gcta in HPC for each phenotype (~250)
gcta --grm-bin /gpfs/data/im-lab/nas40t2/Data/GTEx/V8/genotype/plink_files/GTEX_grm_output --pheno /gpfs/data/im-lab/nas40t2/natasha/gtex_pheno.txt --reml --out /gpfs/data/im-lab/nas40t2/natasha/gtex_output --thread-num 4 --mpheno ___