valid alleles QC

[Sophia20230711]

Hello, I would like to study the genetic correlations of several diseases in East Asians, and below is the log file. I am wondering why so many SNPs are being excluded due to valid alleles QC. Could you help me understand the reason for this exclusion? Thank you.

Reading summary statistics from SLE.sumstats.gz ...
Read summary statistics for 882213 SNPs.
Reading reference panel LD Score from ./eas_ldscores/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1208050 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from ./eas_ldscores/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1208050 SNPs.
After merging with reference panel LD, 882197 SNPs remain.
After merging with regression SNP LD, 882197 SNPs remain.
Computing rg for phenotype 2/2
Reading summary statistics from ref_alt_5968_meta_annovar_1.sumstats.gz ...
Read summary statistics for 1217311 SNPs.
After merging with summary statistics, 882197 SNPs remain.
801434 SNPs with valid alleles.


Heritability of phenotype 1
---------------------------
Total Observed scale h2: 0.6312 (0.0657)
Lambda GC: 1.0833
Mean Chi^2: 1.1788
Intercept: constrained to 1

Heritability of phenotype 2/2
-----------------------------
Total Observed scale h2: -0.0277 (0.045)
Lambda GC: 0.9957
Mean Chi^2: 0.996
Intercept: constrained to 1

Genetic Covariance
------------------
Total Observed scale gencov: -0.1423 (0.0331)
Mean z1*z2: -0.0291
Intercept: constrained to 0

Genetic Correlation
-------------------
Genetic Correlation: nan (nan) (h2  out of bounds) 
Z-score: nan (nan) (h2  out of bounds)
P: nan (nan) (h2  out of bounds)
WARNING: One of the h2's was out of bounds.
This usually indicates a data-munging error or that h2 or N is low.

[aksarkar]

@Sophia20230711 Only SNPs present in both studies are used. It looks like the first study has many fewer variants than the second.

Reading summary statistics from SLE.sumstats.gz ...
Read summary statistics for 882213 SNPs.

Reading summary statistics from ref_alt_5968_meta_annovar_1.sumstats.gz ...
Read summary statistics for 1217311 SNPs.