The munging of 2 summary statistics started at 2025-03-05 09:24:15.202697
Reading in reference file
Reading summary statistics for BMI_EAS_chr1.txt Yengo_Height_EAS_chr1.txt. Please note that this step usually takes a few minutes due to the size of summary statistic files.
All files loaded into R!



Munging file: BMI_EAS_chr1.txt
Interpreting the SNP column as the SNP column.
Interpreting the ALLELE1 column as the A1 column.
Interpreting the ALLELE0 column as the A2 column.
Interpreting the BETA column as the effect column.
Interpreting the INFO column as the INFO column.
Interpreting the PVAL column as the P column.
Interpreting the MAF column as the MAF column.
Interpreting the SE column as the SE column.
Using provided N (163835) for file:BMI_EAS_chr1.txt
Merging file:BMI_EAS_chr1.txt with the reference file:eas_ldscores/w_hm3.snplist
583944 rows present in the full BMI_EAS_chr1.txt summary statistics file.
503019 rows were removed from the BMI_EAS_chr1.txt summary statistics file as the rs-ids for these rows were not present in the reference file.
2402 rows were removed from the BMI_EAS_chr1.txt summary statistics file due to INFO values below the designated threshold of0.9
0 rows were removed from the BMI_EAS_chr1.txt summary statistics file due to missing MAF information or MAFs below the designated threshold of0.01
78523SNPs are left in the summary statistics file BMI_EAS_chr1.txt after QC.
I am done munging file: BMI_EAS_chr1.txt
The file is saved as BMI.sumstats.gz in the current working directory.



Munging file: Yengo_Height_EAS_chr1.txt
Interpreting the RSID column as the SNP column.
Interpreting the EFFECT_ALLELE column as the A1 column.
Interpreting the OTHER_ALLELE column as the A2 column.
Interpreting the BETA column as the effect column.
Interpreting the P column as the P column.
Interpreting the N column as the N column.
Interpreting the MAF column as the MAF column.
Interpreting the SE column as the SE column.
Merging file:Yengo_Height_EAS_chr1.txt with the reference file:eas_ldscores/w_hm3.snplist
89738 rows present in the full Yengo_Height_EAS_chr1.txt summary statistics file.
9613 rows were removed from the Yengo_Height_EAS_chr1.txt summary statistics file as the rs-ids for these rows were not present in the reference file.
1 row(s) were removed from the Yengo_Height_EAS_chr1.txt summary statistics file due to the effect allele (A1) column not matching A1 or A2 in the reference file.
No INFO column, cannot filter on INFO, which may influence results
0 rows were removed from the Yengo_Height_EAS_chr1.txt summary statistics file due to missing MAF information or MAFs below the designated threshold of0.01
80124SNPs are left in the summary statistics file Yengo_Height_EAS_chr1.txt after QC.
I am done munging file: Yengo_Height_EAS_chr1.txt
The file is saved as Height.sumstats.gz in the current working directory.
     
Munging was completed at 2025-03-05 09:24:23.385281
The munging of all files took 0 minutes and 8.1825840473175 seconds
Please check the .log file(s) to ensure that all columns were interpreted correctly and no warnings were issued for any of the summary statistics files