alz

# I decided to use a new Alz analysis that meta-analyzed IGAP Alz data along with UKBB data. Marioni et al, Translational Psychiatry, 2018  (https://www.nature.com/articles/s41398-018-0150-6)

wget http://www.psy.ed.ac.uk/ccace/downloads/UKB_AD_sumstats_17May2018.zip

unzip UKB_AD_sumstats_17May2018.zip

# I looked at the README file in download and the summary stats contain:
SNP
A1 (Effect allele)
Beta (signed summary stat)

# It does not contain sample size
# From the paper: GWAS summary output from the meta-analysis of UK Biobank and IGAP (sample size specified as 314,278 + 74,046 = 388,324)

# It does not contain INFO. Will merge with the LDSC alleles

python ~/my-python-modules/ldsc/munge_sumstats.py --sumstats 4_UK_Biobank_IGAP_17May2018 --merge-alleles ../../../w_hm3.snplist  --out ../Alz_Marioni --N-con 314278 --N-cas 74046

## NOTE ##
- Since analysis, these summary statistics have been corrected by the original authors. A corrected version of these summary statistics can be found here: https://datashare.is.ed.ac.uk/handle/10283/3364
- Check https://doi.org/10.1038/s41398-018-0150-6 for more details


