ldsc.log

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.0
* (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./munge_sumstats.py \
--out ldsc \
--merge-alleles w_hm3.snplist \
--a1-inc  \
--a1 Tested_Allele \
--a2 Other_allele \
--sumstats ldsc.txt 

Interpreting column names as follows:
P:	p-Value
Other_Allele:	Allele 2, interpreted as non-ref allele for signed sumstat.
Tested_Allele:	Allele 1, interpreted as ref allele for signed sumstat.
SNP:	Variant ID (e.g., rs number)
N:	Sample size

Reading list of SNPs for allele merge from w_hm3.snplist
Read 1217311 SNPs for allele merge.
Reading sumstats from ldsc.txt into memory 5000000 SNPs at a time.
WARNING: 1 SNPs had P outside of (0,1]. The P column may be mislabeled.
Read 2348397 SNPs from --sumstats file.
Removed 1323282 SNPs not in --merge-alleles.
Removed 0 SNPs with missing values.
Removed 0 SNPs with INFO <= 0.9.
Removed 0 SNPs with MAF <= 0.01.
Removed 1 SNPs with out-of-bounds p-values.
Removed 0 variants that were not SNPs or were strand-ambiguous.
1025114 SNPs remain.
Removed 2 SNPs with duplicated rs numbers (1025112 SNPs remain).
Removed 0 SNPs with N < 461633.333333 (1025112 SNPs remain).
Removed 0 SNPs whose alleles did not match --merge-alleles (1025112 SNPs remain).
Writing summary statistics for 1217311 SNPs (1025112 with nonmissing beta) to ldsc.sumstats.gz.

Metadata:
Mean chi^2 = 3.465
Lambda GC = 2.566
Max chi^2 = 1416.756
13191 Genome-wide significant SNPs (some may have been removed by filtering).

Conversion finished at Sat Jun 23 00:46:44 2018
Total time elapsed: 8.0h:23.0m:47.25s