SCHEME STDERR
AVERAGEFREQ ON
MINMAXFREQ ON
CUSTOMVARIABLE TotalSampleSize
LABEL TotalSampleSize as N

# LOAD INPUT FILES

# Enable Genomic control correction
GENOMICCONTROL ON
SEPARATOR WHITESPACE


# === DESCRIBE AND PROCESS PROBAND ===
MARKER SNP
ALLELE A1 A2
FREQ MAF
EFFECT Coeff
STDERR se
#PVALUE pVal
#WEIGHT N
PROCESS /mnt/rreal/RDS/acarrasco/ANALYSES_WORKSPACE/GWAS_SURVIVAL/PROBAND/V2/HARMONISED_GWAS_TIMEMIDPOINT_CONFOUNDERS.txt

# === DESCRIBE AND PROCESS OPDC  ===
# Accessing the OPDC GWAS for limb outcome after rerunning with the bug on the limb calculation fixed

MARKER SNP
ALLELE A1 A2
FREQ MAF
EFFECT Coeff
STDERR se
#PVALUE p.value
#WEIGHT N
PROCESS /mnt/rreal/RDS/acarrasco/ANALYSES_WORKSPACE/GWAS_SURVIVAL/OPDC/V2/HARMONISED_GWAS_TIMEMIDPOINT_CONFOUNDERS.txt

# === DESCRIBE AND PROCESS PPMI ===
MARKER SNP
ALLELE A1 A2
FREQ MAF
EFFECT Coeff
STDERR se
#PVALUE p.value
#WEIGHT N
PROCESS /mnt/rreal/RDS/acarrasco/ANALYSES_WORKSPACE/GWAS_SURVIVAL/PPMI/DYSKINESIAS/V2/HARMONISED_GWAS_TIMEMIDPOINT_CONFOUNDERS.txt

# === DESCRIBE AND PROCESS PDBP ===
MARKER SNP
ALLELE A1 A2
FREQ MAF
EFFECT Coeff
STDERR se
#PVALUE pVal
#WEIGHT N
PROCESS /mnt/rreal/RDS/acarrasco/ANALYSES_WORKSPACE/GWAS_SURVIVAL/PDBP/HARMONISED_GWAS_TIMEMIDPOINT_CONFOUNDERS.txt

# === DESCRIBE AND PROCESS PDSTAT ===
MARKER SNP
ALLELE A1 A2
FREQ MAF
EFFECT Coeff
STDERR se
#PVALUE pVal
#WEIGHT N
PROCESS /mnt/rreal/RDS/acarrasco/ANALYSES_WORKSPACE/GWAS_SURVIVAL/PDSTAT/V2/HARMONISED_GWAS_TIMEMIDPOINT_CONFOUNDERS.txt


OUTFILE metal_tpd.opdc.ppmi.pdstat.pdbp_modelConfounders_stderr_ .tbl
ANALYZE HETEROGENEITY

QUIT