epilepsy

From readme file:
# Marker    - this is the marker name
# Allele1   - the first allele for this marker in the first file where it occurs
# Allele2   - the second allele for this marker in the first file where it occurs
# Weight    - the sum of the individual study weights (typically, N) for this marker
# Z-score   - the combined z-statistic for this marker
# P-value   - meta-analysis p-value
# Direction - summary of effect direction for each study, with one '+' or '-' per study
# HetISq    - I^2 statistic which measures heterogeneity on scale of 0-100%
# HetChiSq  - chi-squared statistic in simple test of heterogeneity
# df        - degrees of freedom for heterogeneity statistic
# HetPVal   - P-value for heterogeneity statistic

# Even though this study includes some cohorts of African-American descent, we will still use it

# Since there is no INFO information, I will merge these with the alleles

# I will also treat a1 as the effect allele that the z-score is referring to

~/my-python-modules/ldsc/munge_sumstats.py --sumstats ILAE_All_Epi_11.8.14.txt.gz --out Epilepsy_All --N-col Weight --snp MarkerName --merge-alleles ../../w_hm3.snplist 

~/my-python-modules/ldsc/munge_sumstats.py --sumstats ILAE_Focal_5.8.14.txt.gz --out Epilepsy_Focal --N-col Weight --snp MarkerName --merge-alleles ../../w_hm3.snplist
# Mean ChiSq potentially too small

~/my-python-modules/ldsc/munge_sumstats.py --sumstats ILAE_GGE_5.8.14.txt.gz --out Epilepsy_GGE --N-col Weight --snp MarkerName --merge-alleles ../../w_hm3.snplist  

